libMesh
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This class provides a nice interface to the PETSc C-based data structures for parallel, sparse matrices. More...
#include <petsc_matrix.h>
Public Member Functions | |
PetscMatrix (const Parallel::Communicator &comm_in) | |
Constructor; initializes the matrix to be empty, without any structure, i.e. More... | |
PetscMatrix (Mat m, const Parallel::Communicator &comm_in) | |
Constructor. More... | |
PetscMatrix (PetscMatrix &&)=delete | |
This class manages a C-style struct (Mat) manually, so we don't want to allow any automatic copy/move functions to be generated, and we can't default the destructor. More... | |
PetscMatrix (const PetscMatrix &)=delete | |
PetscMatrix & | operator= (const PetscMatrix &)=delete |
PetscMatrix & | operator= (PetscMatrix &&)=delete |
virtual | ~PetscMatrix () |
void | set_matrix_type (PetscMatrixType mat_type) |
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) override |
Initialize SparseMatrix with the specified sizes. More... | |
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 std::vector< numeric_index_type > &n_nz, const std::vector< numeric_index_type > &n_oz, const numeric_index_type blocksize=1) |
Initialize a PETSc matrix. More... | |
virtual void | init (ParallelType=PARALLEL) override |
Initialize this matrix using the sparsity structure computed by dof_map . More... | |
void | update_preallocation_and_zero () |
Update the sparsity pattern based on dof_map , and set the matrix to zero. More... | |
void | reset_preallocation () |
Reset matrix to use the original nonzero pattern provided by users. More... | |
virtual void | clear () noexcept override |
clear() is called from the destructor, so it should not throw. More... | |
virtual void | zero () override |
Set all entries to 0. More... | |
virtual std::unique_ptr< SparseMatrix< T > > | zero_clone () const override |
virtual std::unique_ptr< SparseMatrix< T > > | clone () const override |
virtual void | zero_rows (std::vector< numeric_index_type > &rows, T diag_value=0.0) override |
Sets all row entries to 0 then puts diag_value in the diagonal entry. More... | |
virtual void | close () override |
Calls the SparseMatrix's internal assembly routines, ensuring that the values are consistent across processors. More... | |
virtual void | flush () override |
For PETSc matrix , this function is similar to close but without shrinking memory. More... | |
virtual numeric_index_type | m () const override |
virtual numeric_index_type | local_m () const final |
Get the number of rows owned by this process. More... | |
virtual numeric_index_type | n () const override |
virtual numeric_index_type | local_n () const final |
Get the number of columns owned by this process. More... | |
void | get_local_size (numeric_index_type &m, numeric_index_type &n) const |
Get the number of rows and columns owned by this process. More... | |
virtual numeric_index_type | row_start () const override |
virtual numeric_index_type | row_stop () const override |
virtual numeric_index_type | col_start () const override |
virtual numeric_index_type | col_stop () const override |
virtual void | set (const numeric_index_type i, const numeric_index_type j, const T value) override |
Set the element (i,j) to value . More... | |
virtual void | add (const numeric_index_type i, const numeric_index_type j, const T value) override |
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) override |
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) override |
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) override |
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) override |
Same as add_block_matrix() , but assumes the row and column maps are the same. More... | |
virtual void | add (const T a, const SparseMatrix< T > &X) override |
Compute A += a*X for scalar a , matrix X . More... | |
virtual void | matrix_matrix_mult (SparseMatrix< T > &X, SparseMatrix< T > &Y, bool reuse=false) override |
Compute Y = A*X for matrix X . More... | |
virtual void | add_sparse_matrix (const SparseMatrix< T > &spm, const std::map< numeric_index_type, numeric_index_type > &row_ltog, const std::map< numeric_index_type, numeric_index_type > &col_ltog, const T scalar) override |
Add scalar* spm to the rows and cols of this matrix (A): A(rows[i], cols[j]) += scalar * spm(i,j) More... | |
virtual T | operator() (const numeric_index_type i, const numeric_index_type j) const override |
virtual Real | l1_norm () const override |
virtual Real | linfty_norm () const override |
virtual bool | closed () const override |
virtual void | set_destroy_mat_on_exit (bool destroy=true) |
If set to false, we don't delete the Mat on destruction and allow instead for PETSc to manage it. More... | |
virtual void | print_personal (std::ostream &os=libMesh::out) const override |
Print the contents of the matrix to the screen with the PETSc viewer. More... | |
virtual void | print_matlab (const std::string &name="") const override |
Print the contents of the matrix in Matlab's sparse matrix format. More... | |
virtual void | print_petsc_binary (const std::string &filename) override |
Write the contents of the matrix to a file in PETSc's binary sparse matrix format. More... | |
virtual void | print_petsc_hdf5 (const std::string &filename) override |
Write the contents of the matrix to a file in PETSc's HDF5 sparse matrix format. More... | |
virtual void | read_petsc_binary (const std::string &filename) override |
Read the contents of the matrix from a file in PETSc's binary sparse matrix format. More... | |
virtual void | read_petsc_hdf5 (const std::string &filename) override |
Read the contents of the matrix from a file in PETSc's HDF5 sparse matrix format. More... | |
virtual void | get_diagonal (NumericVector< T > &dest) const override |
Copies the diagonal part of the matrix into dest . More... | |
virtual void | get_transpose (SparseMatrix< T > &dest) const override |
Copies the transpose of the matrix into dest , which may be *this. More... | |
void | swap (PetscMatrix< T > &) |
Swaps the internal data pointers of two PetscMatrices, no actual values are swapped. More... | |
Mat | mat () |
virtual void | get_row (numeric_index_type i, std::vector< numeric_index_type > &indices, std::vector< T > &values) const override |
Get a row from the matrix. More... | |
virtual void | create_submatrix_nosort (SparseMatrix< T > &submatrix, const std::vector< numeric_index_type > &rows, const std::vector< numeric_index_type > &cols) const override |
Similar to the create_submatrix function, this function creates a submatrix which is defined by the indices given in the rows and cols vectors. More... | |
virtual bool | initialized () const |
void | attach_dof_map (const DofMap &dof_map) |
Set a pointer to the DofMap to use. More... | |
void | attach_sparsity_pattern (const SparsityPattern::Build &sp) |
Set a pointer to a sparsity pattern 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 std::size_t | n_nonzeros () const |
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... | |
template<> | |
void | print (std::ostream &os, const bool sparse) const |
virtual void | read_matlab (const std::string &filename) |
Read the contents of the matrix from 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... | |
const Parallel::Communicator & | comm () 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(), const MatrixBuildType matrix_build_type=MatrixBuildType::AUTOMATIC) |
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_stream=libMesh::out) |
Prints the reference information, by default to libMesh::out . More... | |
static unsigned int | n_objects () |
Prints the number of outstanding (created, but not yet destroyed) objects. More... | |
static void | enable_print_counter_info () |
Methods to enable/disable the reference counter output from print_info() More... | |
static void | disable_print_counter_info () |
Protected Types | |
typedef std::map< std::string, std::pair< unsigned int, unsigned int > > | Counts |
Data structure to log the information. More... | |
Protected Member Functions | |
virtual void | _get_submatrix (SparseMatrix< T > &submatrix, const std::vector< numeric_index_type > &rows, const std::vector< numeric_index_type > &cols, const bool reuse_submatrix) const override |
This function either creates or re-initializes a matrix called submatrix which is defined by the indices given in the rows and cols vectors. More... | |
void | _petsc_viewer (const std::string &filename, PetscViewerType viewertype, PetscFileMode filemode) |
void | increment_constructor_count (const std::string &name) noexcept |
Increments the construction counter. More... | |
void | increment_destructor_count (const std::string &name) noexcept |
Increments the destruction counter. More... | |
Protected Attributes | |
DofMap const * | _dof_map |
The DofMap object associated with this object. More... | |
SparsityPattern::Build const * | _sp |
The sparsity pattern 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... | |
Private Attributes | |
Mat | _mat |
PETSc matrix datatype to store values. More... | |
bool | _destroy_mat_on_exit |
This boolean value should only be set to false for the constructor which takes a PETSc Mat object. More... | |
PetscMatrixType | _mat_type |
std::mutex | _petsc_matrix_mutex |
Threads::spin_mutex | _petsc_matrix_mutex |
This class provides a nice interface to the PETSc C-based data structures for parallel, sparse matrices.
All overridden virtual functions are documented in sparse_matrix.h.
Definition at line 93 of file petsc_matrix.h.
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protectedinherited |
Data structure to log the information.
The log is identified by the class name.
Definition at line 119 of file reference_counter.h.
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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 83 of file petsc_matrix.C.
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explicit |
Constructor.
Creates a PetscMatrix assuming you already have a valid Mat object. In this case, m is NOT destroyed by the PetscMatrix destructor when this object goes out of scope. This allows ownership of m to remain with the original creator, and to simply provide additional functionality with the PetscMatrix.
Definition at line 95 of file petsc_matrix.C.
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delete |
This class manages a C-style struct (Mat) manually, so we don't want to allow any automatic copy/move functions to be generated, and we can't default the destructor.
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delete |
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virtual |
Definition at line 109 of file petsc_matrix.C.
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overrideprotectedvirtual |
This function either creates or re-initializes a matrix called submatrix
which is defined by the indices given in the rows
and cols
vectors.
This function is implemented in terms of MatGetSubMatrix(). The reuse_submatrix
parameter determines whether or not PETSc will treat submatrix
as one which has already been used (had memory allocated) or as a new matrix.
Reimplemented from libMesh::SparseMatrix< T >.
Definition at line 885 of file petsc_matrix.C.
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protected |
Definition at line 738 of file petsc_matrix.C.
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overridevirtual |
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 1234 of file petsc_matrix.C.
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overridevirtual |
Compute A += a*X for scalar a
, matrix X
.
PETSc
will crash!init()
, but also explicitly zero the terms of this
whenever you add a non-zero value to X
.X
will be closed, if not already done, before performing any work. Implements libMesh::SparseMatrix< T >.
Definition at line 1265 of file petsc_matrix.C.
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overridevirtual |
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 from libMesh::SparseMatrix< T >.
Definition at line 841 of file petsc_matrix.C.
Referenced by libMesh::PetscMatrix< libMesh::Number >::add_block_matrix().
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inlineoverridevirtual |
Same as add_block_matrix()
, but assumes the row and column maps are the same.
Thus the matrix dm
must be square.
Reimplemented from libMesh::SparseMatrix< T >.
Definition at line 236 of file petsc_matrix.h.
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overridevirtual |
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 814 of file petsc_matrix.C.
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overridevirtual |
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 1252 of file petsc_matrix.C.
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overridevirtual |
Add scalar*
spm
to the rows and cols of this matrix (A): A(rows[i], cols[j]) += scalar * spm(i,j)
Reimplemented from libMesh::SparseMatrix< T >.
Definition at line 1328 of file petsc_matrix.C.
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inherited |
Set a pointer to the DofMap
to use.
If a separate sparsity pattern is not being used, use the one from the DofMap.
The lifetime of dof_map
must exceed the lifetime of this
.
Definition at line 63 of file sparse_matrix.C.
Referenced by libMesh::__libmesh_tao_hessian(), and libMesh::DofMap::update_sparsity_pattern().
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inherited |
Set a pointer to a sparsity pattern to use.
Useful in cases where a matrix requires a wider (or for efficiency narrower) pattern than most matrices in the system, or in cases where no system sparsity pattern is being calculated by the DofMap.
The lifetime of sp
must exceed the lifetime of this
.
Definition at line 73 of file sparse_matrix.C.
Referenced by libMesh::DofMap::update_sparsity_pattern().
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staticinherited |
Builds a SparseMatrix<T>
using the linear solver package specified by solver_package
.
Definition at line 156 of file sparse_matrix.C.
Referenced by libMesh::TransientRBConstruction::allocate_data_structures(), libMesh::RBConstruction::allocate_data_structures(), libMesh::DofMap::process_mesh_constraint_rows(), ConstraintOperatorTest::test1DCoarseningNewNodes(), ConstraintOperatorTest::test1DCoarseningOperator(), ConstraintOperatorTest::testCoreform(), SystemsTest::testProjectMatrix1D(), SystemsTest::testProjectMatrix2D(), and SystemsTest::testProjectMatrix3D().
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overridevirtualnoexcept |
clear() is called from the destructor, so it should not throw.
Implements libMesh::SparseMatrix< T >.
Definition at line 503 of file petsc_matrix.C.
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overridevirtual |
Implements libMesh::SparseMatrix< T >.
Definition at line 483 of file petsc_matrix.C.
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overridevirtual |
Calls the SparseMatrix's internal assembly routines, ensuring that the values are consistent across processors.
Implements libMesh::SparseMatrix< T >.
Definition at line 1056 of file petsc_matrix.C.
Referenced by libMesh::PetscMatrix< libMesh::Number >::_get_submatrix(), libMesh::PetscMatrix< libMesh::Number >::create_submatrix_nosort(), libMesh::PetscMatrix< libMesh::Number >::get_transpose(), libMesh::libmesh_petsc_snes_jacobian(), libMesh::PetscLinearSolver< Number >::solve_common(), libMesh::SlepcEigenSolver< libMesh::Number >::solve_generalized(), and libMesh::SlepcEigenSolver< libMesh::Number >::solve_standard().
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overridevirtual |
true
if the matrix has been assembled. Implements libMesh::SparseMatrix< T >.
Definition at line 1497 of file petsc_matrix.C.
Referenced by libMesh::PetscMatrix< libMesh::Number >::add().
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overridevirtual |
Implements libMesh::SparseMatrix< T >.
Definition at line 1184 of file petsc_matrix.C.
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overridevirtual |
Implements libMesh::SparseMatrix< T >.
Definition at line 1200 of file petsc_matrix.C.
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inlineinherited |
Parallel::Communicator
object used by this mesh. Definition at line 97 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_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::UniformRefinementEstimator::_estimate_error(), libMesh::Partitioner::_find_global_index_by_pid_map(), libMesh::BoundaryInfo::_find_id_maps(), libMesh::SlepcEigenSolver< libMesh::Number >::_petsc_shell_matrix_get_diagonal(), libMesh::PetscLinearSolver< Number >::_petsc_shell_matrix_get_diagonal(), libMesh::SlepcEigenSolver< libMesh::Number >::_petsc_shell_matrix_mult(), libMesh::PetscLinearSolver< Number >::_petsc_shell_matrix_mult(), libMesh::PetscLinearSolver< Number >::_petsc_shell_matrix_mult_add(), libMesh::MeshRefinement::_refine_elements(), libMesh::MeshRefinement::_smooth_flags(), libMesh::DofMap::add_constraints_to_send_list(), add_cube_convex_hull_to_mesh(), libMesh::PetscDMWrapper::add_dofs_helper(), libMesh::PetscDMWrapper::add_dofs_to_section(), libMesh::TransientRBConstruction::add_IC_to_RB_space(), libMesh::EigenSystem::add_matrices(), libMesh::System::add_matrix(), libMesh::RBConstruction::add_scaled_matrix_and_vector(), libMesh::System::add_variable(), libMesh::System::add_variables(), libMesh::System::add_vector(), libMesh::MeshTools::Modification::all_tri(), libMesh::LaplaceMeshSmoother::allgather_graph(), libMesh::DofMap::allgather_recursive_constraints(), libMesh::TransientRBConstruction::allocate_data_structures(), libMesh::RBConstruction::allocate_data_structures(), libMesh::TransientRBConstruction::assemble_affine_expansion(), libMesh::FEMSystem::assemble_qoi(), libMesh::Nemesis_IO::assert_symmetric_cmaps(), libMesh::MeshCommunication::assign_global_indices(), libMesh::Partitioner::assign_partitioning(), libMesh::MeshTools::Generation::build_extrusion(), libMesh::BoundaryInfo::build_node_list_from_side_list(), libMesh::EquationSystems::build_parallel_elemental_solution_vector(), libMesh::EquationSystems::build_parallel_solution_vector(), libMesh::PetscDMWrapper::build_section(), libMesh::PetscDMWrapper::build_sf(), libMesh::MeshBase::cache_elem_data(), libMesh::System::calculate_norm(), libMesh::DofMap::check_dirichlet_bcid_consistency(), 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::RBConstruction::compute_residual_dual_norm_slow(), libMesh::RBSCMConstruction::compute_SCM_bounds_on_training_set(), libMesh::DofMap::computed_sparsity_already(), libMesh::Problem_Interface::computeF(), libMesh::Problem_Interface::computeJacobian(), libMesh::Problem_Interface::computePreconditioner(), libMesh::ContinuationSystem::ContinuationSystem(), libMesh::MeshBase::copy_constraint_rows(), libMesh::ExodusII_IO::copy_elemental_solution(), libMesh::ExodusII_IO::copy_nodal_solution(), libMesh::ExodusII_IO::copy_scalar_solution(), libMesh::MeshTools::correct_node_proc_ids(), libMesh::MeshTools::create_bounding_box(), libMesh::DofMap::create_dof_constraints(), 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::PetscMatrix< libMesh::Number >::create_submatrix_nosort(), libMesh::MeshCommunication::delete_remote_elements(), libMesh::RBEIMEvaluation::distribute_bfs(), libMesh::DofMap::distribute_dofs(), DMlibMeshFunction(), DMlibMeshJacobian(), DMlibMeshSetSystem_libMesh(), DMVariableBounds_libMesh(), libMesh::DTKSolutionTransfer::DTKSolutionTransfer(), libMesh::MeshRefinement::eliminate_unrefined_patches(), libMesh::RBEIMConstruction::enrich_eim_approximation_on_interiors(), libMesh::RBEIMConstruction::enrich_eim_approximation_on_nodes(), libMesh::RBEIMConstruction::enrich_eim_approximation_on_sides(), libMesh::TransientRBConstruction::enrich_RB_space(), libMesh::EpetraVector< T >::EpetraVector(), AssembleOptimization::equality_constraints(), libMesh::PatchRecoveryErrorEstimator::estimate_error(), libMesh::WeightedPatchRecoveryErrorEstimator::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_error_tolerance(), libMesh::MeshRefinement::flag_elements_by_mean_stddev(), libMesh::MeshRefinement::flag_elements_by_nelem_target(), libMesh::RBEIMEvaluation::gather_bfs(), libMesh::DofMap::gather_constraints(), libMesh::MeshfreeInterpolation::gather_remote_data(), libMesh::CondensedEigenSystem::get_eigenpair(), libMesh::RBEIMEvaluation::get_eim_basis_function_node_value(), libMesh::RBEIMEvaluation::get_eim_basis_function_side_value(), libMesh::RBEIMEvaluation::get_eim_basis_function_value(), libMesh::MeshBase::get_info(), libMesh::System::get_info(), libMesh::DofMap::get_info(), libMesh::ImplicitSystem::get_linear_solver(), libMesh::RBEIMConstruction::get_max_abs_value(), libMesh::RBEIMConstruction::get_node_max_abs_value(), libMesh::RBEIMEvaluation::get_parametrized_function_node_value(), libMesh::RBEIMEvaluation::get_parametrized_function_side_value(), libMesh::RBEIMEvaluation::get_parametrized_function_value(), libMesh::RBEIMConstruction::get_random_point(), AssembleOptimization::inequality_constraints(), AssembleOptimization::inequality_constraints_jacobian(), libMesh::LocationMap< T >::init(), libMesh::TimeSolver::init(), libMesh::SystemSubsetBySubdomain::init(), libMesh::PetscDMWrapper::init_and_attach_petscdm(), libMesh::ExodusII_IO_Helper::initialize(), libMesh::OptimizationSystem::initialize_equality_constraints_storage(), libMesh::OptimizationSystem::initialize_inequality_constraints_storage(), libMesh::RBEIMConstruction::initialize_parametrized_functions_in_training_set(), libMesh::RBEIMConstruction::inner_product(), integrate_function(), libMesh::MeshTools::libmesh_assert_consistent_distributed(), libMesh::MeshTools::libmesh_assert_consistent_distributed_nodes(), libMesh::MeshTools::libmesh_assert_contiguous_dof_ids(), libMesh::MeshTools::libmesh_assert_equal_connectivity(), libMesh::MeshTools::libmesh_assert_equal_points(), libMesh::MeshTools::libmesh_assert_parallel_consistent_new_node_procids(), 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_linesearch_shellfunc(), libMesh::libmesh_petsc_preconditioner_apply(), libMesh::libmesh_petsc_recalculate_monitor(), libMesh::libmesh_petsc_snes_fd_residual(), libMesh::libmesh_petsc_snes_jacobian(), libMesh::libmesh_petsc_snes_mffd_interface(), libMesh::libmesh_petsc_snes_mffd_residual(), libMesh::libmesh_petsc_snes_postcheck(), libMesh::libmesh_petsc_snes_precheck(), libMesh::libmesh_petsc_snes_residual(), 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::LinearImplicitSystem::LinearImplicitSystem(), 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_bcids_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::TriangulatorInterface::MeshedHole::MeshedHole(), LinearElasticityWithContact::move_mesh(), libMesh::DistributedMesh::n_active_elem(), libMesh::MeshTools::n_active_levels(), libMesh::BoundaryInfo::n_boundary_conds(), libMesh::DofMap::n_constrained_dofs(), libMesh::BoundaryInfo::n_edge_conds(), libMesh::CondensedEigenSystem::n_global_non_condensed_dofs(), libMesh::MeshTools::n_levels(), MixedOrderTest::n_neighbor_links(), libMesh::BoundaryInfo::n_nodeset_conds(), libMesh::SparsityPattern::Build::n_nonzeros(), libMesh::MeshTools::n_p_levels(), libMesh::BoundaryInfo::n_shellface_conds(), libMesh::RBEIMEvaluation::node_distribute_bfs(), libMesh::RBEIMEvaluation::node_gather_bfs(), libMesh::RBEIMConstruction::node_inner_product(), libMesh::MeshBase::operator==(), 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::BoundaryInfo::parallel_sync_node_ids(), libMesh::BoundaryInfo::parallel_sync_side_ids(), libMesh::MeshTools::paranoid_n_levels(), libMesh::Partitioner::partition(), 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::DofMap::print_dof_constraints(), libMesh::DofMap::process_mesh_constraint_rows(), libMesh::Partitioner::processor_pairs_to_interface_nodes(), libMesh::InterMeshProjection::project_system_vectors(), FEMParameters::read(), libMesh::Nemesis_IO::read(), libMesh::XdrIO::read(), libMesh::EquationSystems::read(), libMesh::ExodusII_IO::read_header(), libMesh::CheckpointIO::read_header(), libMesh::XdrIO::read_header(), libMesh::System::read_header(), libMesh::RBEIMEvaluation::read_in_interior_basis_functions(), libMesh::RBEIMEvaluation::read_in_node_basis_functions(), libMesh::RBEIMEvaluation::read_in_side_basis_functions(), libMesh::RBEvaluation::read_in_vectors_from_multiple_files(), libMesh::System::read_legacy_data(), libMesh::TransientRBConstruction::read_riesz_representors_from_files(), libMesh::RBConstruction::read_riesz_representors_from_files(), libMesh::System::read_SCALAR_dofs(), libMesh::XdrIO::read_serialized_bc_names(), libMesh::XdrIO::read_serialized_bcs_helper(), libMesh::System::read_serialized_blocked_dof_objects(), libMesh::XdrIO::read_serialized_connectivity(), libMesh::XdrIO::read_serialized_nodes(), libMesh::XdrIO::read_serialized_nodesets(), libMesh::XdrIO::read_serialized_subdomain_names(), libMesh::System::read_serialized_vector(), libMesh::Nemesis_IO_Helper::read_var_names_impl(), libMesh::MeshBase::recalculate_n_partitions(), libMesh::MeshRefinement::refine_and_coarsen_elements(), libMesh::DistributedMesh::renumber_dof_objects(), libMesh::DistributedMesh::renumber_nodes_and_elements(), LinearElasticityWithContact::residual_and_jacobian(), OverlappingAlgebraicGhostingTest::run_ghosting_test(), OverlappingCouplingGhostingTest::run_sparsity_pattern_test(), scale_mesh_and_plot(), libMesh::DofMap::scatter_constraints(), libMesh::CheckpointIO::select_split_config(), libMesh::GenericProjector< FFunctor, GFunctor, FValue, ProjectionAction >::send_and_insert_dof_values(), libMesh::TransientRBConstruction::set_error_temporal_data(), libMesh::Partitioner::set_interface_node_processor_ids_BFS(), libMesh::Partitioner::set_interface_node_processor_ids_linear(), libMesh::Partitioner::set_interface_node_processor_ids_petscpartitioner(), libMesh::Partitioner::set_node_processor_ids(), libMesh::DofMap::set_nonlocal_dof_objects(), libMesh::Partitioner::set_parent_processor_ids(), libMesh::PetscDMWrapper::set_point_range_in_section(), libMesh::PetscDiffSolver::setup_petsc_data(), libMesh::RBEIMEvaluation::side_distribute_bfs(), libMesh::RBEIMEvaluation::side_gather_bfs(), libMesh::RBEIMConstruction::side_inner_product(), libMesh::Partitioner::single_partition(), libMesh::LaplaceMeshSmoother::smooth(), libMesh::split_mesh(), libMesh::RBEIMConstruction::store_eim_solutions_for_training_set(), libMesh::MeshBase::subdomain_ids(), libMesh::BoundaryInfo::sync(), ConstraintOperatorTest::test1DCoarseningNewNodes(), ConstraintOperatorTest::test1DCoarseningOperator(), libMesh::MeshRefinement::test_level_one(), MeshfunctionDFEM::test_mesh_function_dfem(), MeshfunctionDFEM::test_mesh_function_dfem_grad(), MeshFunctionTest::test_p_level(), libMesh::MeshRefinement::test_unflagged(), DofMapTest::testBadElemFECombo(), SystemsTest::testBlockRestrictedVarNDofs(), BoundaryInfoTest::testBoundaryOnChildrenErrors(), ConstraintOperatorTest::testCoreform(), MeshInputTest::testExodusIGASidesets(), MeshTriangulationTest::testFoundCenters(), PointLocatorTest::testLocator(), BoundaryInfoTest::testMesh(), PointLocatorTest::testPlanar(), MeshTriangulationTest::testPoly2TriRefinementBase(), SystemsTest::testProjectCubeWithMeshFunction(), BoundaryInfoTest::testRenumber(), CheckpointIOTest::testSplitter(), MeshInputTest::testTetgenIO(), MeshTriangulationTest::testTriangulatorInterp(), MeshTriangulationTest::testTriangulatorMeshedHoles(), MeshTriangulationTest::testTriangulatorRoundHole(), libMesh::MeshTools::total_weight(), libMesh::RBConstruction::train_reduced_basis_with_POD(), libMesh::MeshFunctionSolutionTransfer::transfer(), libMesh::MeshfreeSolutionTransfer::transfer(), libMesh::Poly2TriTriangulator::triangulate(), libMesh::TransientRBConstruction::truth_assembly(), libMesh::RBConstruction::truth_assembly(), libMesh::MeshRefinement::uniformly_coarsen(), libMesh::TransientRBConstruction::update_RB_initial_condition_all_N(), 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::VTKIO::write_nodal_data(), libMesh::RBEIMEvaluation::write_out_interior_basis_functions(), libMesh::RBEIMEvaluation::write_out_node_basis_functions(), libMesh::RBEIMEvaluation::write_out_side_basis_functions(), libMesh::RBEvaluation::write_out_vectors(), libMesh::TransientRBConstruction::write_riesz_representors_to_files(), libMesh::RBConstruction::write_riesz_representors_to_files(), libMesh::System::write_SCALAR_dofs(), libMesh::XdrIO::write_serialized_bcs_helper(), libMesh::System::write_serialized_blocked_dof_objects(), 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().
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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. Note: The rows
and cols
vectors need to be sorted; Use the nosort version below if rows
and cols
vectors are not sorted; The rows
and cols
only contain indices that are owned by this processor.
Definition at line 469 of file sparse_matrix.h.
Referenced by libMesh::libmesh_petsc_DMCreateInterpolation(), and libMesh::CondensedEigenSystem::solve().
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overridevirtual |
Similar to the create_submatrix
function, this function creates a submatrix
which is defined by the indices given in the rows
and cols
vectors.
Note: Both rows
and cols
can be unsorted; Use the above function for better efficiency if your indices are sorted; rows
and cols
can contain indices that are owned by other processors.
Reimplemented from libMesh::SparseMatrix< T >.
Definition at line 936 of file petsc_matrix.C.
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staticinherited |
Definition at line 100 of file reference_counter.C.
References libMesh::ReferenceCounter::_enable_print_counter.
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staticinherited |
Methods to enable/disable the reference counter output from print_info()
Definition at line 94 of file reference_counter.C.
References libMesh::ReferenceCounter::_enable_print_counter.
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overridevirtual |
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 from libMesh::SparseMatrix< T >.
Definition at line 1071 of file petsc_matrix.C.
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overridevirtual |
Copies the diagonal part of the matrix into dest
.
Implements libMesh::SparseMatrix< T >.
Definition at line 1010 of file petsc_matrix.C.
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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().
void libMesh::PetscMatrix< T >::get_local_size | ( | numeric_index_type & | m, |
numeric_index_type & | n | ||
) | const |
Get the number of rows and columns owned by this process.
i | Row size |
j | Column size |
Definition at line 1135 of file petsc_matrix.C.
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overridevirtual |
Get a row from the matrix.
i | The matrix row to get |
indices | A container that will be filled with the column indices corresponding to (possibly) non-zero values |
values | A container holding the column values |
Implements libMesh::SparseMatrix< T >.
Definition at line 1440 of file petsc_matrix.C.
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overridevirtual |
Copies the transpose of the matrix into dest
, which may be *this.
Implements libMesh::SparseMatrix< T >.
Definition at line 1023 of file petsc_matrix.C.
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inlineprotectednoexceptinherited |
Increments the construction counter.
Should be called in the constructor of any derived class that will be reference counted.
Definition at line 183 of file reference_counter.h.
References libMesh::err, libMesh::BasicOStreamProxy< charT, traits >::get(), libMesh::Quality::name(), and libMesh::Threads::spin_mtx.
Referenced by libMesh::ReferenceCountedObject< RBParametrized >::ReferenceCountedObject().
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inlineprotectednoexceptinherited |
Increments the destruction counter.
Should be called in the destructor of any derived class that will be reference counted.
Definition at line 207 of file reference_counter.h.
References libMesh::err, libMesh::BasicOStreamProxy< charT, traits >::get(), libMesh::Quality::name(), and libMesh::Threads::spin_mtx.
Referenced by libMesh::ReferenceCountedObject< RBParametrized >::~ReferenceCountedObject().
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overridevirtual |
Initialize SparseMatrix with the specified sizes.
m | The global number of rows. |
n | The global number of columns. |
m_l | The local number of rows. |
n_l | The local number of columns. |
nnz | The number of on-diagonal nonzeros per row (defaults to 30). |
noz | The number of off-diagonal nonzeros per row (defaults to 10). |
blocksize | Optional value indicating dense coupled blocks for systems with multiple variables all of the same type. |
Implements libMesh::SparseMatrix< T >.
Definition at line 121 of file petsc_matrix.C.
void libMesh::PetscMatrix< 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 std::vector< numeric_index_type > & | n_nz, | ||
const std::vector< numeric_index_type > & | n_oz, | ||
const numeric_index_type | blocksize = 1 |
||
) |
Initialize a PETSc matrix.
m | The global number of rows. |
n | The global number of columns. |
m_l | The local number of rows. |
n_l | The local number of columns. |
n_nz | array containing the number of nonzeros in each row of the DIAGONAL portion of the local submatrix. |
n_oz | Array containing the number of nonzeros in each row of the OFF-DIAGONAL portion of the local submatrix. |
blocksize | Optional value indicating dense coupled blocks for systems with multiple variables all of the same type. |
Definition at line 237 of file petsc_matrix.C.
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overridevirtual |
Initialize this matrix using the sparsity structure computed by dof_map
.
type | The serial/parallel/ghosted type of the matrix |
Implements libMesh::SparseMatrix< T >.
Definition at line 379 of file petsc_matrix.C.
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inlinevirtualinherited |
true
if the matrix has been initialized, false
otherwise. Definition at line 109 of file sparse_matrix.h.
Referenced by libMesh::PetscMatrix< libMesh::Number >::_get_submatrix(), libMesh::ImplicitSystem::assemble(), and libMesh::System::init_matrices().
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overridevirtual |
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 522 of file petsc_matrix.C.
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overridevirtual |
\( |M|_{\infty} = \max_{i} \sum_{j} |M_{ij}| \)
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 545 of file petsc_matrix.C.
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finalvirtual |
Get the number of rows owned by this process.
Reimplemented from libMesh::SparseMatrix< T >.
Definition at line 1095 of file petsc_matrix.C.
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finalvirtual |
Get the number of columns owned by this process.
Reimplemented from libMesh::SparseMatrix< T >.
Definition at line 1122 of file petsc_matrix.C.
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overridevirtual |
Implements libMesh::SparseMatrix< T >.
Definition at line 1081 of file petsc_matrix.C.
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inline |
Definition at line 323 of file petsc_matrix.h.
Referenced by libMesh::PetscLinearSolver< Number >::init(), libMesh::libmesh_petsc_DMCreateInterpolation(), libMesh::libmesh_petsc_DMCreateRestriction(), libMesh::PetscDiffSolver::solve(), libMesh::TaoOptimizationSolver< T >::solve(), libMesh::PetscNonlinearSolver< Number >::solve(), libMesh::PetscLinearSolver< Number >::solve_common(), libMesh::SlepcEigenSolver< libMesh::Number >::solve_generalized(), and libMesh::SlepcEigenSolver< libMesh::Number >::solve_standard().
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overridevirtual |
Compute Y = A*X for matrix X
.
Set reuse = true if this->_mat and X have the same nonzero pattern as before, and Y is obtained from a previous call to this function with reuse = false
Reimplemented from libMesh::SparseMatrix< T >.
Definition at line 1292 of file petsc_matrix.C.
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overridevirtual |
Implements libMesh::SparseMatrix< T >.
Definition at line 1108 of file petsc_matrix.C.
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virtualinherited |
Definition at line 229 of file sparse_matrix.C.
Referenced by libMesh::SparseMatrix< ValOut >::n_nonzeros().
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inlinestaticinherited |
Prints the number of outstanding (created, but not yet destroyed) objects.
Definition at line 85 of file reference_counter.h.
References libMesh::ReferenceCounter::_n_objects.
Referenced by libMesh::LibMeshInit::~LibMeshInit().
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inlineinherited |
Definition at line 103 of file parallel_object.h.
References libMesh::ParallelObject::_communicator, libMesh::libmesh_assert(), and TIMPI::Communicator::size().
Referenced by libMesh::Partitioner::_find_global_index_by_pid_map(), libMesh::BoundaryInfo::_find_id_maps(), libMesh::DofMap::add_constraints_to_send_list(), libMesh::PetscDMWrapper::add_dofs_to_section(), libMesh::DistributedMesh::add_elem(), libMesh::DofMap::add_neighbors_to_send_list(), libMesh::DistributedMesh::add_node(), libMesh::System::add_vector(), libMesh::LaplaceMeshSmoother::allgather_graph(), libMesh::DofMap::allgather_recursive_constraints(), libMesh::FEMSystem::assembly(), libMesh::Nemesis_IO::assert_symmetric_cmaps(), libMesh::Partitioner::assign_partitioning(), libMesh::AztecLinearSolver< T >::AztecLinearSolver(), libMesh::EquationSystems::build_parallel_elemental_solution_vector(), libMesh::DistributedMesh::clear(), libMesh::DistributedMesh::clear_elems(), libMesh::Nemesis_IO_Helper::compute_border_node_ids(), libMesh::Nemesis_IO_Helper::construct_nemesis_filename(), libMesh::ExodusII_IO::copy_scalar_solution(), libMesh::Nemesis_IO::copy_scalar_solution(), libMesh::UnstructuredMesh::create_pid_mesh(), libMesh::MeshTools::create_processor_bounding_box(), libMesh::DofMap::distribute_dofs(), libMesh::DofMap::distribute_scalar_dofs(), libMesh::DistributedMesh::DistributedMesh(), libMesh::EnsightIO::EnsightIO(), libMesh::RBEIMEvaluation::gather_bfs(), libMesh::MeshBase::get_info(), libMesh::SystemSubsetBySubdomain::init(), libMesh::PetscDMWrapper::init_and_attach_petscdm(), libMesh::Nemesis_IO_Helper::initialize(), libMesh::ExodusII_IO_Helper::initialize(), libMesh::DistributedMesh::insert_elem(), libMesh::MeshTools::libmesh_assert_contiguous_dof_ids(), libMesh::MeshTools::libmesh_assert_parallel_consistent_new_node_procids(), 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::RBEIMEvaluation::node_gather_bfs(), libMesh::Partitioner::partition(), libMesh::MeshBase::partition(), libMesh::Partitioner::partition_unpartitioned_elements(), libMesh::System::point_gradient(), libMesh::System::point_hessian(), libMesh::System::point_value(), libMesh::DofMap::prepare_send_list(), libMesh::DofMap::print_dof_constraints(), libMesh::NameBasedIO::read(), libMesh::Nemesis_IO::read(), libMesh::CheckpointIO::read(), libMesh::CheckpointIO::read_connectivity(), libMesh::XdrIO::read_header(), libMesh::CheckpointIO::read_nodes(), libMesh::System::read_parallel_data(), libMesh::System::read_SCALAR_dofs(), libMesh::System::read_serialized_blocked_dof_objects(), libMesh::System::read_serialized_vector(), libMesh::DistributedMesh::renumber_dof_objects(), libMesh::Partitioner::repartition(), OverlappingFunctorTest::run_partitioner_test(), libMesh::DofMap::scatter_constraints(), libMesh::DistributedMesh::set_next_unique_id(), libMesh::DofMap::set_nonlocal_dof_objects(), libMesh::PetscDMWrapper::set_point_range_in_section(), WriteVecAndScalar::setupTests(), libMesh::RBEIMEvaluation::side_gather_bfs(), DistributedMeshTest::testRemoteElemError(), CheckpointIOTest::testSplitter(), libMesh::MeshRefinement::uniformly_coarsen(), libMesh::DistributedMesh::update_parallel_id_counts(), libMesh::GMVIO::write_binary(), libMesh::GMVIO::write_discontinuous_gmv(), libMesh::ExodusII_IO_Helper::write_nodal_coordinates(), libMesh::VTKIO::write_nodal_data(), libMesh::ExodusII_IO::write_nodal_data(), libMesh::System::write_parallel_data(), libMesh::System::write_SCALAR_dofs(), libMesh::XdrIO::write_serialized_bcs_helper(), libMesh::System::write_serialized_blocked_dof_objects(), libMesh::XdrIO::write_serialized_connectivity(), libMesh::XdrIO::write_serialized_nodes(), and libMesh::XdrIO::write_serialized_nodesets().
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inlinevirtualinherited |
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 138 of file sparse_matrix.h.
Referenced by libMesh::DofMap::attach_matrix(), and libMesh::DofMap::update_sparsity_pattern().
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overridevirtual |
(i,j).Implements libMesh::SparseMatrix< T >.
Definition at line 1383 of file petsc_matrix.C.
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delete |
|
delete |
|
inherited |
Definition at line 122 of file sparse_matrix.C.
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inherited |
Print the contents of the matrix to the screen in a uniform style, regardless of matrix/solver package being used.
Definition at line 238 of file sparse_matrix.C.
Referenced by libMesh::EigenSparseMatrix< T >::print_personal(), and libMesh::LaspackMatrix< T >::print_personal().
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staticinherited |
Prints the reference information, by default to libMesh::out
.
Definition at line 81 of file reference_counter.C.
References libMesh::ReferenceCounter::_enable_print_counter, and libMesh::ReferenceCounter::get_info().
Referenced by libMesh::LibMeshInit::~LibMeshInit().
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overridevirtual |
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 from libMesh::SparseMatrix< T >.
Definition at line 568 of file petsc_matrix.C.
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overridevirtual |
Print the contents of the matrix to the screen with the PETSc viewer.
This function only allows printing to standard out since we have limited ourselves to one PETSc implementation for writing.
Implements libMesh::SparseMatrix< T >.
Definition at line 635 of file petsc_matrix.C.
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overridevirtual |
Write the contents of the matrix to a file in PETSc's binary sparse matrix format.
Reimplemented from libMesh::SparseMatrix< T >.
Definition at line 778 of file petsc_matrix.C.
|
overridevirtual |
Write the contents of the matrix to a file in PETSc's HDF5 sparse matrix format.
Reimplemented from libMesh::SparseMatrix< T >.
Definition at line 788 of file petsc_matrix.C.
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inlineinherited |
Definition at line 114 of file parallel_object.h.
References libMesh::ParallelObject::_communicator, and TIMPI::Communicator::rank().
Referenced by libMesh::BoundaryInfo::_find_id_maps(), libMesh::PetscDMWrapper::add_dofs_to_section(), libMesh::DistributedMesh::add_elem(), libMesh::BoundaryInfo::add_elements(), libMesh::DofMap::add_neighbors_to_send_list(), libMesh::DistributedMesh::add_node(), libMesh::MeshTools::Modification::all_tri(), libMesh::DofMap::allgather_recursive_constraints(), libMesh::FEMSystem::assembly(), libMesh::Nemesis_IO::assert_symmetric_cmaps(), libMesh::Partitioner::assign_partitioning(), libMesh::Nemesis_IO_Helper::build_element_and_node_maps(), libMesh::Partitioner::build_graph(), libMesh::InfElemBuilder::build_inf_elem(), libMesh::BoundaryInfo::build_node_list_from_side_list(), libMesh::EquationSystems::build_parallel_elemental_solution_vector(), libMesh::EquationSystems::build_parallel_solution_vector(), libMesh::DistributedMesh::clear(), libMesh::DistributedMesh::clear_elems(), 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::ExodusII_IO::copy_elemental_solution(), libMesh::ExodusII_IO::copy_nodal_solution(), libMesh::ExodusII_IO::copy_scalar_solution(), libMesh::Nemesis_IO::copy_scalar_solution(), libMesh::MeshTools::correct_node_proc_ids(), libMesh::ExodusII_IO_Helper::create(), libMesh::DistributedMesh::delete_elem(), libMesh::MeshCommunication::delete_remote_elements(), libMesh::DofMap::distribute_dofs(), libMesh::DofMap::distribute_local_dofs_node_major(), libMesh::DofMap::distribute_local_dofs_var_major(), libMesh::DofMap::distribute_scalar_dofs(), libMesh::DistributedMesh::DistributedMesh(), libMesh::DofMap::end_dof(), libMesh::DofMap::end_old_dof(), libMesh::EnsightIO::EnsightIO(), libMesh::GenericProjector< FFunctor, GFunctor, FValue, ProjectionAction >::SubFunctor::find_dofs_to_send(), libMesh::MeshFunction::find_element(), libMesh::MeshFunction::find_elements(), libMesh::UnstructuredMesh::find_neighbors(), libMesh::DofMap::first_dof(), libMesh::DofMap::first_old_dof(), libMesh::RBEIMEvaluation::gather_bfs(), 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::DofMap::get_local_constraints(), libMesh::Nemesis_IO_Helper::get_node_cmap(), libMesh::Nemesis_IO_Helper::get_node_map(), libMesh::Nemesis_IO_Helper::get_ns_param_global(), libMesh::Nemesis_IO_Helper::get_ss_param_global(), libMesh::SparsityPattern::Build::handle_vi_vj(), libMesh::LaplaceMeshSmoother::init(), libMesh::SystemSubsetBySubdomain::init(), libMesh::PetscDMWrapper::init_and_attach_petscdm(), HeatSystem::init_data(), 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::RBSCMEvaluation::legacy_write_offline_data_to_files(), libMesh::RBEvaluation::legacy_write_offline_data_to_files(), libMesh::MeshTools::libmesh_assert_consistent_distributed(), libMesh::MeshTools::libmesh_assert_consistent_distributed_nodes(), libMesh::MeshTools::libmesh_assert_contiguous_dof_ids(), libMesh::MeshTools::libmesh_assert_parallel_consistent_procids< Elem >(), 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::TriangulatorInterface::MeshedHole::MeshedHole(), libMesh::MeshBase::n_active_local_elem(), libMesh::BoundaryInfo::n_boundary_conds(), libMesh::BoundaryInfo::n_edge_conds(), libMesh::DofMap::n_local_dofs(), 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::RBEIMEvaluation::node_gather_bfs(), libMesh::SparsityPattern::Build::operator()(), libMesh::DistributedMesh::own_node(), libMesh::BoundaryInfo::parallel_sync_node_ids(), libMesh::BoundaryInfo::parallel_sync_side_ids(), libMesh::System::point_gradient(), libMesh::System::point_hessian(), libMesh::System::point_value(), libMesh::DofMap::print_dof_constraints(), libMesh::DofMap::process_mesh_constraint_rows(), 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::EquationSystems::read(), libMesh::ExodusII_IO_Helper::read_elem_num_map(), libMesh::ExodusII_IO_Helper::read_global_values(), libMesh::ExodusII_IO::read_header(), libMesh::CheckpointIO::read_header(), libMesh::XdrIO::read_header(), libMesh::System::read_header(), libMesh::System::read_legacy_data(), libMesh::DynaIO::read_mesh(), libMesh::ExodusII_IO_Helper::read_node_num_map(), libMesh::System::read_parallel_data(), libMesh::TransientRBConstruction::read_riesz_representors_from_files(), libMesh::RBConstruction::read_riesz_representors_from_files(), libMesh::System::read_SCALAR_dofs(), libMesh::XdrIO::read_serialized_bc_names(), libMesh::XdrIO::read_serialized_bcs_helper(), libMesh::System::read_serialized_blocked_dof_objects(), libMesh::XdrIO::read_serialized_connectivity(), libMesh::System::read_serialized_data(), libMesh::XdrIO::read_serialized_nodes(), libMesh::XdrIO::read_serialized_nodesets(), libMesh::XdrIO::read_serialized_subdomain_names(), libMesh::System::read_serialized_vector(), libMesh::System::read_serialized_vectors(), libMesh::Nemesis_IO_Helper::read_var_names_impl(), libMesh::DistributedMesh::renumber_dof_objects(), libMesh::DistributedMesh::renumber_nodes_and_elements(), libMesh::DofMap::scatter_constraints(), libMesh::CheckpointIO::select_split_config(), libMesh::DistributedMesh::set_next_unique_id(), libMesh::DofMap::set_nonlocal_dof_objects(), libMesh::PetscDMWrapper::set_point_range_in_section(), libMesh::RBEIMEvaluation::side_gather_bfs(), ExodusTest< elem_type >::test_read_gold(), ExodusTest< elem_type >::test_write(), MeshInputTest::testAbaqusRead(), MeshInputTest::testCopyElementSolutionImpl(), MeshInputTest::testCopyElementVectorImpl(), MeshInputTest::testCopyNodalSolutionImpl(), DefaultCouplingTest::testCoupling(), PointNeighborCouplingTest::testCoupling(), MeshInputTest::testDynaFileMappings(), MeshInputTest::testDynaNoSplines(), MeshInputTest::testDynaReadElem(), MeshInputTest::testDynaReadPatch(), MeshInputTest::testExodusFileMappings(), MeshInputTest::testExodusIGASidesets(), MeshInputTest::testExodusWriteElementDataFromDiscontinuousNodalData(), MeshInputTest::testLowOrderEdgeBlocks(), SystemsTest::testProjectMatrix1D(), SystemsTest::testProjectMatrix2D(), SystemsTest::testProjectMatrix3D(), BoundaryInfoTest::testShellFaceConstraints(), MeshInputTest::testSingleElementImpl(), WriteVecAndScalar::testSolution(), CheckpointIOTest::testSplitter(), MeshInputTest::testTetgenIO(), libMesh::MeshTools::total_weight(), libMesh::MeshRefinement::uniformly_coarsen(), libMesh::DistributedMesh::update_parallel_id_counts(), libMesh::DTKAdapter::update_variable_values(), 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_element_values_element_major(), libMesh::ExodusII_IO_Helper::write_elements(), libMesh::ExodusII_IO_Helper::write_elemset_data(), libMesh::ExodusII_IO_Helper::write_elemsets(), libMesh::ExodusII_IO::write_global_data(), libMesh::ExodusII_IO_Helper::write_global_values(), libMesh::System::write_header(), 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::VTKIO::write_nodal_data(), libMesh::ExodusII_IO::write_nodal_data(), libMesh::ExodusII_IO::write_nodal_data_common(), libMesh::ExodusII_IO::write_nodal_data_discontinuous(), libMesh::ExodusII_IO_Helper::write_nodal_values(), libMesh::ExodusII_IO_Helper::write_nodeset_data(), libMesh::Nemesis_IO_Helper::write_nodesets(), libMesh::ExodusII_IO_Helper::write_nodesets(), libMesh::RBEIMEvaluation::write_out_interior_basis_functions(), libMesh::RBEIMEvaluation::write_out_node_basis_functions(), libMesh::RBEIMEvaluation::write_out_side_basis_functions(), write_output_solvedata(), libMesh::System::write_parallel_data(), libMesh::RBConstruction::write_riesz_representors_to_files(), libMesh::System::write_SCALAR_dofs(), libMesh::XdrIO::write_serialized_bc_names(), libMesh::XdrIO::write_serialized_bcs_helper(), libMesh::System::write_serialized_blocked_dof_objects(), libMesh::XdrIO::write_serialized_connectivity(), libMesh::System::write_serialized_data(), libMesh::XdrIO::write_serialized_nodes(), libMesh::XdrIO::write_serialized_nodesets(), libMesh::XdrIO::write_serialized_subdomain_names(), libMesh::System::write_serialized_vector(), libMesh::System::write_serialized_vectors(), libMesh::ExodusII_IO_Helper::write_sideset_data(), 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().
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virtualinherited |
Read the contents of the matrix from Matlab's sparse matrix format.
If the size and sparsity of the matrix in filename
appears consistent with the existing sparsity of this
then the existing parallel decomposition and sparsity will be retained. If not, then this
will be initialized with the sparsity from the file, linearly partitioned onto the number of processors available.
Definition at line 502 of file sparse_matrix.C.
Referenced by ConstraintOperatorTest::test1DCoarseningNewNodes(), and ConstraintOperatorTest::testCoreform().
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overridevirtual |
Read the contents of the matrix from a file in PETSc's binary sparse matrix format.
Reimplemented from libMesh::SparseMatrix< T >.
Definition at line 798 of file petsc_matrix.C.
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overridevirtual |
Read the contents of the matrix from a file in PETSc's HDF5 sparse matrix format.
Reimplemented from libMesh::SparseMatrix< T >.
Definition at line 806 of file petsc_matrix.C.
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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 500 of file sparse_matrix.h.
void libMesh::PetscMatrix< T >::reset_preallocation | ( | ) |
Reset matrix to use the original nonzero pattern provided by users.
Definition at line 402 of file petsc_matrix.C.
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overridevirtual |
Implements libMesh::SparseMatrix< T >.
Definition at line 1152 of file petsc_matrix.C.
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overridevirtual |
Implements libMesh::SparseMatrix< T >.
Definition at line 1168 of file petsc_matrix.C.
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overridevirtual |
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 1216 of file petsc_matrix.C.
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virtual |
If set to false, we don't delete the Mat on destruction and allow instead for PETSc
to manage it.
Definition at line 1511 of file petsc_matrix.C.
void libMesh::PetscMatrix< T >::set_matrix_type | ( | PetscMatrixType | mat_type | ) |
Definition at line 115 of file petsc_matrix.C.
void libMesh::PetscMatrix< T >::swap | ( | PetscMatrix< T > & | m_in | ) |
Swaps the internal data pointers of two PetscMatrices, no actual values are swapped.
Definition at line 1518 of file petsc_matrix.C.
Referenced by libMesh::__libmesh_petsc_diff_solver_jacobian().
void libMesh::PetscMatrix< T >::update_preallocation_and_zero | ( | ) |
Update the sparsity pattern based on dof_map
, and set the matrix to zero.
This is useful in cases where the sparsity pattern changes during a computation.
Definition at line 396 of file petsc_matrix.C.
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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 146 of file sparse_matrix.h.
Referenced by libMesh::DofMap::update_sparsity_pattern().
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inherited |
Multiplies the matrix by the NumericVector arg
and stores the result in NumericVector dest
.
Definition at line 200 of file sparse_matrix.C.
Referenced by libMesh::TransientRBConstruction::add_IC_to_RB_space(), libMesh::RBSCMConstruction::Aq_inner_product(), libMesh::RBSCMConstruction::B_inner_product(), libMesh::RBConstruction::compute_Fq_representor_innerprods(), libMesh::RBConstruction::compute_output_dual_innerprods(), libMesh::RBConstruction::compute_residual_dual_norm_slow(), libMesh::TransientRBConstruction::enrich_RB_space(), libMesh::RBConstruction::enrich_RB_space(), AssembleOptimization::gradient(), libMesh::TransientRBConstruction::mass_matrix_scaled_matvec(), AssembleOptimization::objective(), libMesh::RBConstruction::print_basis_function_orthogonality(), libMesh::ImplicitSystem::qoi_parameter_hessian(), libMesh::ImplicitSystem::qoi_parameter_hessian_vector_product(), libMesh::TransientRBConstruction::set_error_temporal_data(), libMesh::RBConstruction::train_reduced_basis_with_POD(), libMesh::TransientRBConstruction::truth_assembly(), libMesh::RBConstruction::truth_solve(), libMesh::TransientRBConstruction::update_RB_system_matrices(), libMesh::RBConstruction::update_RB_system_matrices(), libMesh::TransientRBConstruction::update_residual_terms(), and libMesh::RBConstruction::update_residual_terms().
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inherited |
Multiplies the matrix by the NumericVector arg
and adds the result to the NumericVector dest
.
Definition at line 210 of file sparse_matrix.C.
Referenced by libMesh::ImplicitSystem::weighted_sensitivity_adjoint_solve().
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overridevirtual |
Set all entries to 0.
Implements libMesh::SparseMatrix< T >.
Definition at line 417 of file petsc_matrix.C.
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overridevirtual |
Implements libMesh::SparseMatrix< T >.
Definition at line 461 of file petsc_matrix.C.
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overridevirtual |
Sets all row entries to 0 then puts diag_value
in the diagonal entry.
Reimplemented from libMesh::SparseMatrix< T >.
Definition at line 438 of file petsc_matrix.C.
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protectedinherited |
Definition at line 120 of file parallel_object.h.
Referenced by libMesh::EquationSystems::build_parallel_elemental_solution_vector(), libMesh::EquationSystems::build_parallel_solution_vector(), libMesh::ParallelObject::comm(), libMesh::ParallelObject::n_processors(), libMesh::ParallelObject::operator=(), libMesh::ParallelObject::processor_id(), and libMesh::BoundaryInfo::regenerate_id_sets().
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staticprotectedinherited |
Actually holds the data.
Definition at line 124 of file reference_counter.h.
Referenced by libMesh::ReferenceCounter::get_info().
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private |
This boolean value should only be set to false
for the constructor which takes a PETSc Mat object.
Definition at line 373 of file petsc_matrix.h.
Referenced by libMesh::PetscMatrix< libMesh::Number >::swap().
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protectedinherited |
The DofMap
object associated with this object.
May be queried for degree-of-freedom counts on processors.
Definition at line 567 of file sparse_matrix.h.
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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().
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protectedinherited |
Flag indicating whether or not the matrix has been initialized.
Definition at line 579 of file sparse_matrix.h.
Referenced by libMesh::PetscMatrix< libMesh::Number >::_get_submatrix(), libMesh::PetscMatrix< libMesh::Number >::create_submatrix_nosort(), libMesh::EpetraMatrix< T >::EpetraMatrix(), libMesh::PetscMatrix< libMesh::Number >::get_transpose(), and libMesh::SparseMatrix< ValOut >::initialized().
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private |
PETSc matrix datatype to store values.
Definition at line 367 of file petsc_matrix.h.
Referenced by libMesh::PetscMatrix< libMesh::Number >::_get_submatrix(), libMesh::PetscMatrix< libMesh::Number >::add(), libMesh::PetscMatrix< libMesh::Number >::create_submatrix_nosort(), libMesh::PetscMatrix< libMesh::Number >::get_transpose(), libMesh::PetscMatrix< libMesh::Number >::mat(), and libMesh::PetscMatrix< libMesh::Number >::swap().
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private |
Definition at line 375 of file petsc_matrix.h.
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staticprotectedinherited |
Mutual exclusion object to enable thread-safe reference counting.
Definition at line 137 of file reference_counter.h.
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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().
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mutableprivate |
Definition at line 378 of file petsc_matrix.h.
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mutableprivate |
Definition at line 380 of file petsc_matrix.h.
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protectedinherited |
The sparsity
pattern associated with this object.
Should be queried for entry counts (or with need_full_sparsity_pattern, patterns) when needed.
Definition at line 574 of file sparse_matrix.h.