This class allows to use a PETSc shell matrix as a PetscMatrix. More...

#include <petsc_matrix_shell_matrix.h>

Inheritance diagram for libMesh::PetscMatrixShellMatrix< T >:

Public Member Functions
	PetscMatrixShellMatrix (const Parallel::Communicator &comm_in)

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=30, const numeric_index_type=10, const numeric_index_type blocksize=1) override
	Initialize SparseMatrix with the specified sizes. More...

virtual void	init (ParallelType=PARALLEL) override
	Initialize this matrix using the sparsity structure computed by `dof_map`. More...

virtual SparseMatrix< T > &	operator= (const SparseMatrix< T > &) override
	This looks like a copy assignment operator, but note that, unlike normal copy assignment operators, it is pure virtual. More...

virtual bool	require_sparsity_pattern () const override

virtual SolverPackage	solver_package () override

Mat	mat ()

Mat	mat () const

virtual void	clear () noexcept override
	clear() is called from the destructor, so it should not throw. More...

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...

void	swap (PetscMatrixBase< T > &)
	Swaps the internal data pointers of two PetscMatrices, no actual values are swapped. More...

void	set_context ()
	Set the context (ourself) for `_mat`. 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...

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	close () override
	Calls the SparseMatrix's internal assembly routines, ensuring that the values are consistent across processors. More...

virtual bool	closed () const override

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 void	zero ()=0
	Set all entries to 0. More...

virtual std::unique_ptr< SparseMatrix< T > >	zero_clone () const =0

virtual std::unique_ptr< SparseMatrix< T > >	clone () const =0

virtual void	zero_rows (std::vector< numeric_index_type > &rows, T diag_value=0.0)
	Sets all row entries to 0 then puts `diag_value` in the diagonal entry. More...

virtual void	flush ()
	For PETSc matrix , this function is similar to close but without shrinking memory. More...

virtual void	set (const numeric_index_type i, const numeric_index_type j, const T value)=0
	Set the element (i,j) to `value`. More...

virtual void	add (const numeric_index_type i, const numeric_index_type j, const T value)=0
	Add `value` to the element (i,j). More...

virtual void	add (const T a, const SparseMatrix< T > &X)=0
	Compute \( A \leftarrow A + a*X \) for scalar `a`, matrix `X`. More...

virtual void	add_matrix (const DenseMatrix< T > &dm, const std::vector< numeric_index_type > &rows, const std::vector< numeric_index_type > &cols)=0
	Add the full matrix `dm` to the SparseMatrix. More...

virtual void	add_matrix (const DenseMatrix< T > &dm, const std::vector< numeric_index_type > &dof_indices)=0
	Same as `add_matrix`, but assumes the row and column maps are the same. More...

virtual void	add_block_matrix (const DenseMatrix< T > &dm, const std::vector< numeric_index_type > &brows, const std::vector< numeric_index_type > &bcols)
	Add the full matrix `dm` to the SparseMatrix. More...

virtual void	add_block_matrix (const DenseMatrix< T > &dm, const std::vector< numeric_index_type > &dof_indices)
	Same as `add_block_matrix()`, but assumes the row and column maps are the same. More...

virtual void	matrix_matrix_mult (SparseMatrix< T > &, SparseMatrix< T > &, bool)
	Compute Y = A*X for matrix `X`. More...

virtual void	add_sparse_matrix (const SparseMatrix< T > &, const std::map< numeric_index_type, numeric_index_type > &, const std::map< numeric_index_type, numeric_index_type > &, const T)
	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 =0

virtual Real	l1_norm () const =0

virtual Real	linfty_norm () const =0

Real	l1_norm_diff (const SparseMatrix< T > &other_mat) const

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	print_personal (std::ostream &os=libMesh::out) const =0
	Print the contents of the matrix to the screen in a package-personalized style, if available. More...

virtual void	print_matlab (const std::string &="") const
	Print the contents of the matrix in Matlab's sparse matrix format. More...

virtual void	print_petsc_binary (const std::string &filename)
	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)
	Write the contents of the matrix to a file in PETSc's HDF5 sparse matrix format. More...

virtual void	read (const std::string &filename)
	Read the contents of the matrix from a file, with the file format inferred from the extension of `filename`. More...

virtual void	read_matlab (const std::string &filename)
	Read the contents of the matrix from the Matlab-script sparse matrix format used by PETSc. More...

virtual void	read_petsc_binary (const std::string &filename)
	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)
	Read the contents of the matrix from a file in PETSc's HDF5 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	create_submatrix_nosort (SparseMatrix< T > &, const std::vector< numeric_index_type > &, const std::vector< numeric_index_type > &) const
	Similar to the above function, this function creates a `submatrix` which is defined by the indices given in the `rows` and `cols` vectors. More...

virtual void	reinit_submatrix (SparseMatrix< T > &submatrix, const std::vector< numeric_index_type > &rows, const std::vector< numeric_index_type > &cols) const
	This function is similar to the one above, but it allows you to reuse the existing sparsity pattern of "submatrix" instead of reallocating it again. More...

void	vector_mult (NumericVector< T > &dest, const NumericVector< T > &arg) const
	Multiplies the matrix by the NumericVector `arg` and stores the result in NumericVector `dest`. More...

void	vector_mult_add (NumericVector< T > &dest, const NumericVector< T > &arg) const
	Multiplies the matrix by the NumericVector `arg` and adds the result to the NumericVector `dest`. More...

virtual void	get_diagonal (NumericVector< T > &dest) const =0
	Copies the diagonal part of the matrix into `dest`. More...

virtual void	get_transpose (SparseMatrix< T > &dest) const =0
	Copies the transpose of the matrix into `dest`, which may be *this. More...

virtual void	get_row (numeric_index_type i, std::vector< numeric_index_type > &indices, std::vector< T > &values) const =0
	Get a row from the matrix. More...

virtual void	scale (const T scale)
	Scales all elements of this matrix by `scale`. More...

virtual bool	supports_hash_table () const

void	use_hash_table (bool use_hash)
	Sets whether to use hash table assembly. More...

bool	use_hash_table () const

virtual void	restore_original_nonzero_pattern ()
	Reset the memory storage of the matrix. More...

const Parallel::Communicator &	comm () const

processor_id_type	n_processors () const

processor_id_type	processor_id () const

Static Public Member Functions
static PetscMatrixBase< T > *	get_context (Mat mat, const TIMPI::Communicator &comm)

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 > &, const std::vector< numeric_index_type > &, const std::vector< numeric_index_type > &, const bool) const
	Protected implementation of the create_submatrix and reinit_submatrix routines. More...

void	increment_constructor_count (const std::string &name) noexcept
	Increments the construction counter. More...

void	increment_destructor_count (const std::string &name) noexcept
	Increments the destruction counter. More...

Protected 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...

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...

bool	_use_hash_table
	Flag indicating whether the matrix is assembled using a hash table. 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
const bool	_omit_constrained_dofs
	Whether to omit constrained degrees of freedom. More...

Friends
void	init_shell_mat (PetscMatrixShellMatrix< T > &obj)

void	init_shell_mat (PetscMatrixShellMatrix< T > &obj, 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 blocksize_in)

Detailed Description

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

This class allows to use a PETSc shell matrix as a PetscMatrix.

Author: Alexander Lindsay

Date: 2024

Definition at line 38 of file petsc_matrix_shell_matrix.h.

Member Typedef Documentation

◆ Counts

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

protectedinherited

Data structure to log the information.

The log is identified by the class name.

Definition at line 119 of file reference_counter.h.

Constructor & Destructor Documentation

◆ PetscMatrixShellMatrix()

template<typename T >

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

explicit

Definition at line 81 of file petsc_matrix_shell_matrix.h.

   : PetscMatrixBase<T>(comm_in), _omit_constrained_dofs(false)
 {
 }

Member Function Documentation

◆ _get_submatrix()

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 629 of file sparse_matrix.h.

Referenced by libMesh::SparseMatrix< ValOut >::create_submatrix(), and libMesh::SparseMatrix< ValOut >::reinit_submatrix().

   {
     libmesh_not_implemented();
   }

◆ add() [1/2]

template<typename T>

virtual void libMesh::SparseMatrix< T >::add	(	const numeric_index_type	i,
		const numeric_index_type	j,
		const T	value
	)

pure virtualinherited

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.

Implemented in libMesh::StaticCondensation, libMesh::PetscMatrix< T >, libMesh::EpetraMatrix< T >, libMesh::DiagonalMatrix< T >, libMesh::LaspackMatrix< T >, libMesh::EigenSparseMatrix< T >, libMesh::StaticCondensation, libMesh::PetscMFFDMatrix< T >, libMesh::PetscMFFDMatrix< Number >, and libMesh::LumpedMassMatrix< T >.

Referenced by add_M_C_K_helmholtz(), libMesh::RBConstruction::add_scaled_Aq(), libMesh::TransientRBConstruction::add_scaled_mass_matrix(), assemble_shell(), libMesh::NewmarkSystem::compute_matrix(), libMesh::RBConstruction::compute_residual_dual_norm_slow(), AssembleOptimization::hessian(), libMesh::HDGProblem::jacobian(), libMesh::RBSCMConstruction::load_matrix_B(), LinearElasticityWithContact::residual_and_jacobian(), libMesh::ClawSystem::solve_conservation_law(), SystemsTest::testProjectMatrix1D(), SystemsTest::testProjectMatrix2D(), SystemsTest::testProjectMatrix3D(), libMesh::TransientRBConstruction::truth_assembly(), and libMesh::RBConstruction::truth_assembly().

◆ add() [2/2]

template<typename T>

virtual void libMesh::SparseMatrix< T >::add	(	const T	a,
		const SparseMatrix< T > &	X
	)

pure virtualinherited

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

Implemented in libMesh::StaticCondensation, libMesh::PetscMatrix< T >, libMesh::EpetraMatrix< T >, libMesh::LaspackMatrix< T >, libMesh::DiagonalMatrix< T >, libMesh::EigenSparseMatrix< T >, libMesh::StaticCondensation, libMesh::PetscMFFDMatrix< T >, libMesh::PetscMFFDMatrix< Number >, and libMesh::LumpedMassMatrix< T >.

◆ add_block_matrix() [1/2]

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 91 of file sparse_matrix.C.

Referenced by libMesh::SparseMatrix< ValOut >::add_block_matrix().

 {
   libmesh_assert_equal_to (dm.m() / brows.size(), dm.n() / bcols.size());
 
   const numeric_index_type blocksize = cast_int<numeric_index_type>
     (dm.m() / brows.size());
 
   libmesh_assert_equal_to (dm.m()%blocksize, 0);
   libmesh_assert_equal_to (dm.n()%blocksize, 0);
 
   std::vector<numeric_index_type> rows, cols;
 
   rows.reserve(blocksize*brows.size());
   cols.reserve(blocksize*bcols.size());
 
   for (auto & row : brows)
     {
       numeric_index_type i = row * blocksize;
 
       for (unsigned int v=0; v<blocksize; v++)
         rows.push_back(i++);
     }
 
   for (auto & col : bcols)
     {
       numeric_index_type j = col * blocksize;
 
       for (unsigned int v=0; v<blocksize; v++)
         cols.push_back(j++);
     }
 
   this->add_matrix (dm, rows, cols);
 }

◆ add_block_matrix() [2/2]

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 337 of file sparse_matrix.h.

339 { this->add_block_matrix (dm, dof_indices, dof_indices); }

libMesh::SparseMatrix::add_block_matrix

virtual void add_block_matrix(const DenseMatrix< T > &dm, const std::vector< numeric_index_type > &brows, const std::vector< numeric_index_type > &bcols)

Add the full matrix dm to the SparseMatrix.

Definition: sparse_matrix.C:91

◆ add_matrix() [1/2]

template<typename T>

virtual void libMesh::SparseMatrix< T >::add_matrix	(	const DenseMatrix< T > &	dm,
		const std::vector< numeric_index_type > &	rows,
		const std::vector< numeric_index_type > &	cols
	)

pure virtualinherited

Add the full matrix dm to the SparseMatrix.

This is useful for adding an element matrix at assembly time.

Implemented in libMesh::StaticCondensation, libMesh::PetscMatrix< T >, libMesh::EpetraMatrix< T >, libMesh::DiagonalMatrix< T >, libMesh::LaspackMatrix< T >, libMesh::EigenSparseMatrix< T >, libMesh::StaticCondensation, libMesh::PetscMFFDMatrix< T >, and libMesh::PetscMFFDMatrix< Number >.

Referenced by libMesh::HDGProblem::add_matrix(), libMesh::RBConstruction::add_scaled_matrix_and_vector(), assemble(), LinearElasticity::assemble(), assemble_1D(), AssembleOptimization::assemble_A_and_F(), assemble_biharmonic(), assemble_divgrad(), assemble_elasticity(), assemble_ellipticdg(), assemble_func(), assemble_graddiv(), assemble_helmholtz(), assemble_laplace(), assemble_mass(), assemble_matrices(), assemble_matrix_and_rhs(), assemble_poisson(), assemble_SchroedingerEquation(), assemble_shell(), assemble_stokes(), assemble_wave(), assembly_with_dg_fem_context(), compute_jacobian(), fe_assembly(), LaplaceYoung::jacobian(), LargeDeformationElasticity::jacobian(), periodic_bc_test_poisson(), Biharmonic::JR::residual_and_jacobian(), LinearElasticityWithContact::residual_and_jacobian(), and OverlappingCouplingGhostingTest::run_sparsity_pattern_test().

◆ add_matrix() [2/2]

template<typename T>

virtual void libMesh::SparseMatrix< T >::add_matrix	(	const DenseMatrix< T > &	dm,
		const std::vector< numeric_index_type > &	dof_indices
	)

pure virtualinherited

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

Thus the matrix dm must be square.

Implemented in libMesh::StaticCondensation, libMesh::PetscMatrix< T >, libMesh::EpetraMatrix< T >, libMesh::DiagonalMatrix< T >, libMesh::LaspackMatrix< T >, libMesh::EigenSparseMatrix< T >, libMesh::StaticCondensation, libMesh::PetscMFFDMatrix< T >, and libMesh::PetscMFFDMatrix< Number >.

◆ add_sparse_matrix()

template<typename T>

virtual void libMesh::SparseMatrix< T >::add_sparse_matrix	(	const SparseMatrix< T > &	,
		const std::map< numeric_index_type, numeric_index_type > &	,
		const std::map< numeric_index_type, numeric_index_type > &	,
		const T
	)

inlinevirtualinherited

Add scalar* spm to the rows and cols of this matrix (A): A(rows[i], cols[j]) += scalar * spm(i,j)

Reimplemented in libMesh::PetscMatrix< T >.

Definition at line 356 of file sparse_matrix.h.

360 { libmesh_not_implemented(); }

◆ attach_dof_map()

template<typename T >

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

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 72 of file sparse_matrix.C.

Referenced by libMesh::__libmesh_tao_hessian(), DMlibMeshJacobian(), libMesh::libmesh_petsc_snes_jacobian(), and libMesh::DofMap::update_sparsity_pattern().

 {
   _dof_map = &dof_map;
   if (!_sp)
     _sp = dof_map.get_sparsity_pattern();
 }

◆ attach_sparsity_pattern()

template<typename T >

void libMesh::SparseMatrix< T >::attach_sparsity_pattern ( const SparsityPattern::Build & sp )

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 82 of file sparse_matrix.C.

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

 {
   _sp = &sp;
 }

◆ build()

template<typename T >

std::unique_ptr< SparseMatrix< T > > libMesh::SparseMatrix< T >::build	(	const Parallel::Communicator &	comm,
		const SolverPackage	solver_package = `libMesh::default_solver_package()`,
		const MatrixBuildType	matrix_build_type = `MatrixBuildType::AUTOMATIC`
	)

staticinherited

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

Definition at line 165 of file sparse_matrix.C.

Referenced by libMesh::CondensedEigenSystem::add_matrices(), libMesh::System::add_matrix(), libMesh::TransientRBConstruction::allocate_data_structures(), libMesh::RBConstruction::allocate_data_structures(), libMesh::CondensedEigenSystem::copy_super_to_sub(), libMesh::StaticCondensation::init(), main(), libMesh::DofMap::process_mesh_constraint_rows(), ConstraintOperatorTest::test1DCoarseningNewNodes(), ConstraintOperatorTest::test1DCoarseningOperator(), ConstraintOperatorTest::testCoreform(), ConnectedComponentsTest::testEdge(), SystemsTest::testProjectMatrix1D(), SystemsTest::testProjectMatrix2D(), and SystemsTest::testProjectMatrix3D().

 {
   // Avoid unused parameter warnings when no solver packages are enabled.
   libmesh_ignore(comm);
 
   if (matrix_build_type == MatrixBuildType::DIAGONAL)
     return std::make_unique<DiagonalMatrix<T>>(comm);
 
   // Build the appropriate vector
   switch (solver_package)
     {
 
 #ifdef LIBMESH_HAVE_LASPACK
     case LASPACK_SOLVERS:
       return std::make_unique<LaspackMatrix<T>>(comm);
 #endif
 
 
 #ifdef LIBMESH_HAVE_PETSC
     case PETSC_SOLVERS:
       return std::make_unique<PetscMatrix<T>>(comm);
 #endif
 
 
 #ifdef LIBMESH_TRILINOS_HAVE_EPETRA
     case TRILINOS_SOLVERS:
       return std::make_unique<EpetraMatrix<T>>(comm);
 #endif
 
 
 #ifdef LIBMESH_HAVE_EIGEN
     case EIGEN_SOLVERS:
       return std::make_unique<EigenSparseMatrix<T>>(comm);
 #endif
 
     default:
       libmesh_error_msg("ERROR:  Unrecognized solver package: " << solver_package);
     }
 }

◆ clear()

template<typename T >

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

overridevirtualnoexceptinherited

clear() is called from the destructor, so it should not throw.

Implements libMesh::SparseMatrix< T >.

Reimplemented in libMesh::StaticCondensation, and libMesh::StaticCondensation.

Definition at line 74 of file petsc_matrix_base.C.

Referenced by libMesh::StaticCondensation::clear().

 {
   if ((this->initialized()) && (this->_destroy_mat_on_exit))
     {
       exceptionless_semiparallel_only();
 
       // If we encounter an error here, print a warning but otherwise
       // keep going since we may be recovering from an exception.
       PetscErrorCode ierr = MatDestroy (&_mat);
       if (ierr)
         libmesh_warning("Warning: MatDestroy returned a non-zero error code which we ignored.");
 
       this->_is_initialized = false;
     }
 }

◆ clone()

template<typename T>

virtual std::unique_ptr<SparseMatrix<T> > libMesh::SparseMatrix< T >::clone ( ) const

pure virtualinherited

Returns: A smart pointer to a copy of this matrix.

Note: This must be overridden in the derived classes.

Implemented in libMesh::StaticCondensation, libMesh::PetscMatrix< T >, libMesh::EpetraMatrix< T >, libMesh::DiagonalMatrix< T >, libMesh::LaspackMatrix< T >, libMesh::EigenSparseMatrix< T >, libMesh::StaticCondensation, libMesh::PetscMFFDMatrix< T >, libMesh::PetscMFFDMatrix< Number >, and libMesh::LumpedMassMatrix< T >.

◆ close()

template<typename T >

void libMesh::PetscMatrixBase< T >::close ( )

overridevirtualinherited

Calls the SparseMatrix's internal assembly routines, ensuring that the values are consistent across processors.

Implements libMesh::SparseMatrix< T >.

Reimplemented in libMesh::StaticCondensation, and libMesh::StaticCondensation.

Definition at line 226 of file petsc_matrix_base.C.

Referenced by libMesh::PetscMatrix< T >::_get_submatrix(), libMesh::PetscMatrix< T >::create_submatrix_nosort(), DMlibMeshJacobian(), libMesh::PetscMatrix< T >::get_transpose(), libMesh::libmesh_petsc_snes_jacobian(), and libMesh::PetscLinearSolver< Number >::solve_common().

 {
   semiparallel_only();
 
   // BSK - 1/19/2004
   // strictly this check should be OK, but it seems to
   // fail on matrix-free matrices.  Do they falsely
   // state they are assembled?  Check with the developers...
   //   if (this->closed())
   //     return;
 
   MatAssemblyBeginEnd(this->comm(), this->_mat, MAT_FINAL_ASSEMBLY);
 }

◆ closed()

template<typename T >

bool libMesh::PetscMatrixBase< T >::closed ( ) const

overridevirtualinherited

Returns: true if the matrix has been assembled.

Implements libMesh::SparseMatrix< T >.

Reimplemented in libMesh::StaticCondensation, and libMesh::StaticCondensation.

Definition at line 241 of file petsc_matrix_base.C.

Referenced by libMesh::PetscMatrix< T >::add().

 {
   libmesh_assert (this->initialized());
 
   PetscBool assembled;
 
   LibmeshPetscCall(MatAssembled(this->_mat, &assembled));
 
   return (assembled == PETSC_TRUE);
 }

◆ col_start()

template<typename T >

numeric_index_type libMesh::PetscMatrixBase< T >::col_start ( ) const

overridevirtualinherited

Returns: The index of the first matrix column owned by this processor.

Implements libMesh::SparseMatrix< T >.

Reimplemented in libMesh::StaticCondensation, and libMesh::StaticCondensation.

Definition at line 202 of file petsc_matrix_base.C.

 {
   libmesh_assert (this->initialized());
 
   PetscInt start=0, stop=0;
 
   LibmeshPetscCall(MatGetOwnershipRangeColumn(this->_mat, &start, &stop));
 
   return static_cast<numeric_index_type>(start);
 }

◆ col_stop()

template<typename T >

numeric_index_type libMesh::PetscMatrixBase< T >::col_stop ( ) const

overridevirtualinherited

Returns: The index of the last matrix column (+1) owned by this processor.

Implements libMesh::SparseMatrix< T >.

Reimplemented in libMesh::StaticCondensation, and libMesh::StaticCondensation.

Definition at line 214 of file petsc_matrix_base.C.

 {
   libmesh_assert (this->initialized());
 
   PetscInt start=0, stop=0;
 
   LibmeshPetscCall(MatGetOwnershipRangeColumn(this->_mat, &start, &stop));
 
   return static_cast<numeric_index_type>(stop);
 }

◆ comm()

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

inlineinherited

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

Definition at line 97 of file parallel_object.h.

References libMesh::ParallelObject::_communicator.

98 { return _communicator; }

libMesh::ParallelObject::_communicator

const Parallel::Communicator & _communicator

Definition: parallel_object.h:120

◆ create_submatrix()

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 PetscMatrixBase subclasses. 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 509 of file sparse_matrix.h.

Referenced by libMesh::CondensedEigenSystem::copy_super_to_sub(), libMesh::libmesh_petsc_DMCreateInterpolation(), and libMesh::CondensedEigenSystem::solve().

   {
     this->_get_submatrix(submatrix,
                          rows,
                          cols,
                          false); // false means DO NOT REUSE submatrix
   }

◆ create_submatrix_nosort()

template<typename T>

virtual void libMesh::SparseMatrix< T >::create_submatrix_nosort	(	SparseMatrix< T > &	,
		const std::vector< numeric_index_type > &	,
		const std::vector< numeric_index_type > &
	)		const

inlinevirtualinherited

Similar to the above 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 in libMesh::PetscMatrix< T >.

Definition at line 527 of file sparse_matrix.h.

   {
     libmesh_not_implemented();
   }

◆ disable_print_counter_info()

void libMesh::ReferenceCounter::disable_print_counter_info ( )

staticinherited

Definition at line 100 of file reference_counter.C.

References libMesh::ReferenceCounter::_enable_print_counter.

 {
   _enable_print_counter = false;
   return;
 }

◆ enable_print_counter_info()

void libMesh::ReferenceCounter::enable_print_counter_info ( )

staticinherited

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

Definition at line 94 of file reference_counter.C.

References libMesh::ReferenceCounter::_enable_print_counter.

 {
   _enable_print_counter = true;
   return;
 }

◆ flush()

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 244 of file sparse_matrix.h.

244 { close(); }

libMesh::SparseMatrix::close

virtual void close()=0

Calls the SparseMatrix's internal assembly routines, ensuring that the values are consistent across p...

◆ get_context()

template<typename T >

PetscMatrixBase< T > * libMesh::PetscMatrixBase< T >::get_context	(	Mat	mat,
		const TIMPI::Communicator &	comm
	)

staticinherited

Returns: The context for mat if it exists, else a nullptr

Definition at line 116 of file petsc_matrix_base.C.

Referenced by DMlibMeshJacobian(), form_matrixA(), and libMesh::libmesh_petsc_snes_jacobian().

 {
   void * ctx;
   PetscContainer container;
   LibmeshPetscCall2(comm, PetscObjectQuery((PetscObject)mat, "PetscMatrixCtx", (PetscObject *)&container));
   if (!container)
     return nullptr;
 
   LibmeshPetscCall2(comm, PetscContainerGetPointer(container, &ctx));
   libmesh_assert(ctx);
   return static_cast<PetscMatrixBase<T> *>(ctx);
 }

◆ get_diagonal()

template<typename T>

virtual void libMesh::SparseMatrix< T >::get_diagonal ( NumericVector< T > & dest ) const

pure virtualinherited

Copies the diagonal part of the matrix into dest.

Implemented in libMesh::StaticCondensation, libMesh::PetscMatrix< T >, libMesh::EpetraMatrix< T >, libMesh::LaspackMatrix< T >, libMesh::DiagonalMatrix< T >, libMesh::EigenSparseMatrix< T >, libMesh::StaticCondensation, libMesh::PetscMFFDMatrix< T >, and libMesh::PetscMFFDMatrix< Number >.

Referenced by libMesh::LumpedMassMatrix< T >::add(), and libMesh::DiagonalMatrix< T >::add().

◆ get_info()

std::string libMesh::ReferenceCounter::get_info ( )

staticinherited

Gets a string containing the reference information.

Definition at line 47 of file reference_counter.C.

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

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

 {
 #if defined(LIBMESH_ENABLE_REFERENCE_COUNTING) && defined(DEBUG)
 
   std::ostringstream oss;
 
   oss << '\n'
       << " ---------------------------------------------------------------------------- \n"
       << "| Reference count information                                                |\n"
       << " ---------------------------------------------------------------------------- \n";
 
   for (const auto & [name, cd] : _counts)
     oss << "| " << name << " reference count information:\n"
         << "|  Creations:    " << cd.first    << '\n'
         << "|  Destructions: " << cd.second << '\n';
 
   oss << " ---------------------------------------------------------------------------- \n";
 
   return oss.str();
 
 #else
 
   return "";
 
 #endif
 }

◆ get_row()

template<typename T>

virtual void libMesh::SparseMatrix< T >::get_row	(	numeric_index_type	i,
		std::vector< numeric_index_type > &	indices,
		std::vector< T > &	values
	)		const

pure virtualinherited

Get a row from the matrix.

Parameters

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

Implemented in libMesh::StaticCondensation, libMesh::PetscMatrix< T >, libMesh::EpetraMatrix< T >, libMesh::LaspackMatrix< T >, libMesh::DiagonalMatrix< T >, libMesh::EigenSparseMatrix< T >, libMesh::StaticCondensation, libMesh::PetscMFFDMatrix< T >, and libMesh::PetscMFFDMatrix< Number >.

Referenced by libMesh::MeshBase::copy_constraint_rows().

◆ get_transpose()

template<typename T>

virtual void libMesh::SparseMatrix< T >::get_transpose ( SparseMatrix< T > & dest ) const

pure virtualinherited

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

Implemented in libMesh::StaticCondensation, libMesh::PetscMatrix< T >, libMesh::EpetraMatrix< T >, libMesh::LaspackMatrix< T >, libMesh::DiagonalMatrix< T >, libMesh::EigenSparseMatrix< T >, libMesh::StaticCondensation, libMesh::PetscMFFDMatrix< T >, and libMesh::PetscMFFDMatrix< Number >.

Referenced by libMesh::EigenSparseLinearSolver< T >::adjoint_solve(), libMesh::LinearSolver< Number >::adjoint_solve(), and libMesh::ImplicitSystem::weighted_sensitivity_adjoint_solve().

◆ increment_constructor_count()

void libMesh::ReferenceCounter::increment_constructor_count ( const std::string & name )

inlineprotectednoexceptinherited

Increments the construction counter.

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

Definition at line 183 of file reference_counter.h.

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

Referenced by libMesh::ReferenceCountedObject< RBParametrized >::ReferenceCountedObject().

 {
   libmesh_try
   {
     Threads::spin_mutex::scoped_lock lock(Threads::spin_mtx);
     std::pair<unsigned int, unsigned int> & p = _counts[name];
     p.first++;
   }
   libmesh_catch (...)
   {
     auto stream = libMesh::err.get();
     stream->exceptions(stream->goodbit); // stream must not throw
     libMesh::err << "Encountered unrecoverable error while calling "
                  << "ReferenceCounter::increment_constructor_count() "
                  << "for a(n) " << name << " object." << std::endl;
     std::terminate();
   }
 }

◆ increment_destructor_count()

void libMesh::ReferenceCounter::increment_destructor_count ( const std::string & name )

inlineprotectednoexceptinherited

Increments the destruction counter.

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

Definition at line 207 of file reference_counter.h.

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

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

 {
   libmesh_try
   {
     Threads::spin_mutex::scoped_lock lock(Threads::spin_mtx);
     std::pair<unsigned int, unsigned int> & p = _counts[name];
     p.second++;
   }
   libmesh_catch (...)
   {
     auto stream = libMesh::err.get();
     stream->exceptions(stream->goodbit); // stream must not throw
     libMesh::err << "Encountered unrecoverable error while calling "
                  << "ReferenceCounter::increment_destructor_count() "
                  << "for a(n) " << name << " object." << std::endl;
     std::terminate();
   }
 }

◆ init() [1/2]

template<typename T >

void libMesh::PetscMatrixShellMatrix< 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`
	)

overridevirtual

Initialize SparseMatrix with the specified sizes.

Parameters

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 >.

Reimplemented in libMesh::StaticCondensation, and libMesh::StaticCondensation.

Definition at line 30 of file petsc_matrix_shell_matrix.C.

Referenced by libMesh::StaticCondensation::init().

 {
   init_shell_mat(*this, m, n, m_l, n_l, blocksize);
   this->set_context();
 }

◆ init() [2/2]

template<typename T>

virtual void libMesh::PetscMatrixShellMatrix< T >::init ( ParallelType = PARALLEL )

overridevirtual

Initialize this matrix using the sparsity structure computed by dof_map.

Parameters

type	The serial/parallel/ghosted type of the matrix

Implements libMesh::SparseMatrix< T >.

Reimplemented in libMesh::StaticCondensation, and libMesh::StaticCondensation.

◆ initialized()

template<typename T>

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

inlinevirtualinherited

Returns: true if the matrix has been initialized, false otherwise.

Reimplemented in libMesh::StaticCondensation.

Definition at line 133 of file sparse_matrix.h.

Referenced by libMesh::PetscMatrix< T >::_get_submatrix(), libMesh::ImplicitSystem::assemble(), libMesh::System::init_matrices(), and libMesh::StaticCondensation::initialized().

133 { return _is_initialized; }

libMesh::SparseMatrix::_is_initialized

bool _is_initialized

Flag indicating whether or not the matrix has been initialized.

Definition: sparse_matrix.h:653

◆ l1_norm()

template<typename T>

virtual Real libMesh::SparseMatrix< T >::l1_norm ( ) const

pure virtualinherited

Returns: The \( \ell_1 \)-norm of the matrix, that is the max column sum: \( |M|_1 = \max_{j} \sum_{i} |M_{ij}| \)

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

Implemented in libMesh::StaticCondensation, libMesh::PetscMatrix< T >, libMesh::EpetraMatrix< T >, libMesh::LaspackMatrix< T >, libMesh::DiagonalMatrix< T >, libMesh::EigenSparseMatrix< T >, libMesh::StaticCondensation, libMesh::PetscMFFDMatrix< T >, and libMesh::PetscMFFDMatrix< Number >.

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

◆ l1_norm_diff()

template<typename T>

Real libMesh::SparseMatrix< T >::l1_norm_diff ( const SparseMatrix< T > & other_mat ) const

inherited

Returns: The l1_norm() of the difference of this and other_mat

Definition at line 879 of file sparse_matrix.C.

 {
   auto diff_mat = this->clone();
   diff_mat->add(-1.0, other_mat);
   return diff_mat->l1_norm();
 }

◆ linfty_norm()

template<typename T>

virtual Real libMesh::SparseMatrix< T >::linfty_norm ( ) const

pure virtualinherited

Returns: The \( \ell_{\infty} \)-norm of the matrix, that is the max row sum:

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

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

Implemented in libMesh::StaticCondensation, libMesh::PetscMatrix< T >, libMesh::EpetraMatrix< T >, libMesh::LaspackMatrix< T >, libMesh::DiagonalMatrix< T >, libMesh::EigenSparseMatrix< T >, libMesh::StaticCondensation, libMesh::PetscMFFDMatrix< T >, and libMesh::PetscMFFDMatrix< Number >.

Referenced by SystemsTest::testProjectMatrix1D(), SystemsTest::testProjectMatrix2D(), and SystemsTest::testProjectMatrix3D().

◆ local_m()

template<typename T >

numeric_index_type libMesh::PetscMatrixBase< T >::local_m ( ) const

finalvirtualinherited

Get the number of rows owned by this process.

Reimplemented from libMesh::SparseMatrix< T >.

Definition at line 142 of file petsc_matrix_base.C.

 {
   libmesh_assert (this->initialized());
 
   PetscInt m = 0;
 
   LibmeshPetscCall(MatGetLocalSize (this->_mat, &m, NULL));
 
   return static_cast<numeric_index_type>(m);
 }

◆ local_n()

template<typename T >

numeric_index_type libMesh::PetscMatrixBase< T >::local_n ( ) const

finalvirtualinherited

Get the number of columns owned by this process.

Reimplemented from libMesh::SparseMatrix< T >.

Definition at line 166 of file petsc_matrix_base.C.

 {
   libmesh_assert (this->initialized());
 
   PetscInt n = 0;
 
   LibmeshPetscCall(MatGetLocalSize (this->_mat, NULL, &n));
 
   return static_cast<numeric_index_type>(n);
 }

◆ m()

template<typename T >

numeric_index_type libMesh::PetscMatrixBase< T >::m ( ) const

overridevirtualinherited

Returns: The row-dimension of the matrix.

Implements libMesh::SparseMatrix< T >.

Reimplemented in libMesh::StaticCondensation, and libMesh::StaticCondensation.

Definition at line 130 of file petsc_matrix_base.C.

 {
   libmesh_assert (this->initialized());
 
   PetscInt petsc_m=0, petsc_n=0;
 
   LibmeshPetscCall(MatGetSize (this->_mat, &petsc_m, &petsc_n));
 
   return static_cast<numeric_index_type>(petsc_m);
 }

◆ mat() [1/2]

template<typename T>

Mat libMesh::PetscMatrixBase< T >::mat ( )

inlineinherited

Returns: The raw PETSc matrix pointer.

Note: This is generally not required in user-level code.; Don't do anything crazy like calling MatDestroy() on it, or very bad things will likely happen!

Definition at line 120 of file petsc_matrix_base.h.

Referenced by libMesh::StaticCondensation::add_matrix(), libMesh::PetscLinearSolver< Number >::init(), libMesh::libmesh_petsc_DMCreateInterpolation(), libMesh::libmesh_petsc_DMCreateRestriction(), libMesh::PetscDiffSolver::solve(), libMesh::TaoOptimizationSolver< T >::solve(), libMesh::PetscNonlinearSolver< Number >::solve(), and libMesh::PetscLinearSolver< Number >::solve_common().

120 { libmesh_assert (_mat); return _mat; }

libMesh::libmesh_assert

libmesh_assert(ctx)

libMesh::PetscMatrixBase::_mat

Mat _mat

PETSc matrix datatype to store values.

Definition: petsc_matrix_base.h:180

◆ mat() [2/2]

template<typename T>

Mat libMesh::PetscMatrixBase< T >::mat ( ) const

inlineinherited

Definition at line 121 of file petsc_matrix_base.h.

121 { libmesh_assert(_mat); return _mat; }

libMesh::libmesh_assert

libmesh_assert(ctx)

libMesh::PetscMatrixBase::_mat

Mat _mat

PETSc matrix datatype to store values.

Definition: petsc_matrix_base.h:180

◆ matrix_matrix_mult()

template<typename T>

virtual void libMesh::SparseMatrix< T >::matrix_matrix_mult	(	SparseMatrix< T > &	,
		SparseMatrix< T > &	,
		bool
	)

inlinevirtualinherited

Compute Y = A*X for matrix X.

Reimplemented in libMesh::PetscMatrix< T >.

Definition at line 349 of file sparse_matrix.h.

350 { libmesh_not_implemented(); }

◆ n()

template<typename T >

numeric_index_type libMesh::PetscMatrixBase< T >::n ( ) const

overridevirtualinherited

Returns: The column-dimension of the matrix.

Implements libMesh::SparseMatrix< T >.

Reimplemented in libMesh::StaticCondensation, and libMesh::StaticCondensation.

Definition at line 154 of file petsc_matrix_base.C.

 {
   libmesh_assert (this->initialized());
 
   PetscInt petsc_m=0, petsc_n=0;
 
   LibmeshPetscCall(MatGetSize (this->_mat, &petsc_m, &petsc_n));
 
   return static_cast<numeric_index_type>(petsc_n);
 }

◆ n_nonzeros()

template<typename T >

std::size_t libMesh::SparseMatrix< T >::n_nonzeros ( ) const

virtualinherited

Returns: the global number of non-zero entries in the matrix sparsity pattern

Definition at line 238 of file sparse_matrix.C.

Referenced by libMesh::SparseMatrix< ValOut >::n_nonzeros().

 {
   if (!_sp)
     return 0;
   return _sp->n_nonzeros();
 }

◆ n_objects()

static unsigned int libMesh::ReferenceCounter::n_objects ( )

inlinestaticinherited

Prints the number of outstanding (created, but not yet destroyed) objects.

Definition at line 85 of file reference_counter.h.

References libMesh::ReferenceCounter::_n_objects.

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

86 { return _n_objects; }

libMesh::ReferenceCounter::_n_objects

static Threads::atomic< unsigned int > _n_objects

The number of objects.

Definition: reference_counter.h:132

◆ n_processors()

processor_id_type libMesh::ParallelObject::n_processors ( ) const

inlineinherited

Returns: The number of processors in the group.

Definition at line 103 of file parallel_object.h.

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

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

◆ need_full_sparsity_pattern()

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 PetscMatrixBase subclasses. 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 162 of file sparse_matrix.h.

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

163 { return false; }

◆ operator()()

template<typename T>

virtual T libMesh::SparseMatrix< T >::operator()	(	const numeric_index_type	i,
		const numeric_index_type	j
	)		const

pure virtualinherited

Returns: A copy of matrix entry (i,j).

Note: This may be an expensive operation, and you should always be careful where you call this function.

Implemented in libMesh::StaticCondensation, libMesh::PetscMatrix< T >, libMesh::EpetraMatrix< T >, libMesh::LaspackMatrix< T >, libMesh::DiagonalMatrix< T >, libMesh::EigenSparseMatrix< T >, libMesh::StaticCondensation, libMesh::PetscMFFDMatrix< T >, and libMesh::PetscMFFDMatrix< Number >.

◆ operator=()

template<typename T>

SparseMatrix< T > & libMesh::PetscMatrixShellMatrix< T >::operator= ( const SparseMatrix< T > & )

overridevirtual

This looks like a copy assignment operator, but note that, unlike normal copy assignment operators, it is pure virtual.

This function should be overridden in derived classes so that they can be copied correctly via references to the base class. This design usually isn't a good idea in general, but in this context it works because we usually don't have a mix of different kinds of SparseMatrix active in the library at a single time.

Returns: A reference to *this as the base type.

Reimplemented from libMesh::SparseMatrix< T >.

Definition at line 88 of file petsc_matrix_shell_matrix.h.

 {
   libmesh_error();
 }

◆ print() [1/2]

template<>

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

inherited

Definition at line 131 of file sparse_matrix.C.

 {
   // std::complex<>::operator<<() is defined, but use this form
 
   if (sparse)
     {
       libmesh_not_implemented();
     }
 
   os << "Real part:" << std::endl;
   for (auto i : make_range(this->m()))
     {
       for (auto j : make_range(this->n()))
         os << std::setw(8) << (*this)(i,j).real() << " ";
       os << std::endl;
     }
 
   os << std::endl << "Imaginary part:" << std::endl;
   for (auto i : make_range(this->m()))
     {
       for (auto j : make_range(this->n()))
         os << std::setw(8) << (*this)(i,j).imag() << " ";
       os << std::endl;
     }
 }

◆ print() [2/2]

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 247 of file sparse_matrix.C.

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

 {
   parallel_object_only();
 
   libmesh_assert (this->initialized());
 
   const numeric_index_type first_dof = this->row_start(),
                            end_dof   = this->row_stop();
 
   // We'll print the matrix from processor 0 to make sure
   // it's serialized properly
   if (this->processor_id() == 0)
     {
       libmesh_assert_equal_to (first_dof, 0);
       for (numeric_index_type i : make_range(end_dof))
         {
           if (sparse)
             {
               for (auto j : make_range(this->n()))
                 {
                   T c = (*this)(i,j);
                   if (c != static_cast<T>(0.0))
                     {
                       os << i << " " << j << " " << c << std::endl;
                     }
                 }
             }
           else
             {
               for (auto j : make_range(this->n()))
                 os << (*this)(i,j) << " ";
               os << std::endl;
             }
         }
 
       std::vector<numeric_index_type> ibuf, jbuf;
       std::vector<T> cbuf;
       numeric_index_type currenti = end_dof;
       for (auto p : IntRange<processor_id_type>(1, this->n_processors()))
         {
           this->comm().receive(p, ibuf);
           this->comm().receive(p, jbuf);
           this->comm().receive(p, cbuf);
           libmesh_assert_equal_to (ibuf.size(), jbuf.size());
           libmesh_assert_equal_to (ibuf.size(), cbuf.size());
 
           if (ibuf.empty())
             continue;
           libmesh_assert_greater_equal (ibuf.front(), currenti);
           libmesh_assert_greater_equal (ibuf.back(), ibuf.front());
 
           std::size_t currentb = 0;
           for (;currenti <= ibuf.back(); ++currenti)
             {
               if (sparse)
                 {
                   for (numeric_index_type j=0; j<this->n(); j++)
                     {
                       if (currentb < ibuf.size() &&
                           ibuf[currentb] == currenti &&
                           jbuf[currentb] == j)
                         {
                           os << currenti << " " << j << " " << cbuf[currentb] << std::endl;
                           currentb++;
                         }
                     }
                 }
               else
                 {
                   for (auto j : make_range(this->n()))
                     {
                       if (currentb < ibuf.size() &&
                           ibuf[currentb] == currenti &&
                           jbuf[currentb] == j)
                         {
                           os << cbuf[currentb] << " ";
                           currentb++;
                         }
                       else
                         os << static_cast<T>(0.0) << " ";
                     }
                   os << std::endl;
                 }
             }
         }
       if (!sparse)
         {
           for (; currenti != this->m(); ++currenti)
             {
               for (numeric_index_type j=0; j<this->n(); j++)
                 os << static_cast<T>(0.0) << " ";
               os << std::endl;
             }
         }
     }
   else
     {
       std::vector<numeric_index_type> ibuf, jbuf;
       std::vector<T> cbuf;
 
       // We'll assume each processor has access to entire
       // matrix rows, so (*this)(i,j) is valid if i is a local index.
       for (numeric_index_type i : make_range(first_dof, end_dof))
         {
           for (auto j : make_range(this->n()))
             {
               T c = (*this)(i,j);
               if (c != static_cast<T>(0.0))
                 {
                   ibuf.push_back(i);
                   jbuf.push_back(j);
                   cbuf.push_back(c);
                 }
             }
         }
       this->comm().send(0,ibuf);
       this->comm().send(0,jbuf);
       this->comm().send(0,cbuf);
     }
 }

◆ print_info()

void libMesh::ReferenceCounter::print_info ( std::ostream & out_stream = libMesh::out )

staticinherited

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

Definition at line 81 of file reference_counter.C.

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

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

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

◆ print_matlab()

template<typename T >

void libMesh::SparseMatrix< T >::print_matlab ( const std::string & name = "" ) const

virtualinherited

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 370 of file sparse_matrix.C.

 {
   parallel_object_only();
 
   libmesh_assert (this->initialized());
 
   const numeric_index_type first_dof = this->row_start(),
                            end_dof   = this->row_stop();
 
   // We'll print the matrix from processor 0 to make sure
   // it's serialized properly
   if (this->processor_id() == 0)
     {
       std::unique_ptr<std::ofstream> file;
 
       if (name != "")
         file = std::make_unique<std::ofstream>(name.c_str());
 
       std::ostream & os = (name == "") ? libMesh::out : *file;
 
       std::size_t sparsity_nonzeros = this->n_nonzeros();
 
       std::size_t real_nonzeros = 0;
 
       libmesh_assert_equal_to(first_dof, 0);
       for (numeric_index_type i : make_range(end_dof))
         {
           for (auto j : make_range(this->n()))
             {
               T c = (*this)(i,j);
               if (c != static_cast<T>(0.0))
                 ++real_nonzeros;
             }
         }
 
 
       for (auto p : IntRange<processor_id_type>(1, this->n_processors()))
         {
           std::size_t nonzeros_on_p = 0;
           this->comm().receive(p, nonzeros_on_p);
           real_nonzeros += nonzeros_on_p;
         }
 
       if (sparsity_nonzeros &&
           sparsity_nonzeros != real_nonzeros)
         libmesh_warning(sparsity_nonzeros <<
                         " nonzeros allocated, but " <<
                         real_nonzeros << " used.");
 
       // We probably want to be more consistent than that, if our
       // sparsity is overallocated.
 
       // Print a header similar to PETSc's mat_view ascii_matlab
       os << "%Mat Object: () " << this->n_processors() << " MPI processes\n"
          << "%  type: " << (this->n_processors() > 1 ? "mpi" : "seq") << "aij\n"
          << "% Size = " << this->m() << ' ' << this->n() << '\n'
          << "% Nonzeros = " << real_nonzeros << '\n'
          << "zzz = zeros(" << real_nonzeros << ",3);\n"
          << "zzz = [\n";
 
       for (numeric_index_type i : make_range(end_dof))
         {
           // FIXME - we need a base class way to iterate over a
           // SparseMatrix row.
           for (auto j : make_range(this->n()))
             {
               T c = (*this)(i,j);
               if (c != static_cast<T>(0.0))
                 {
                   // Convert from 0-based to 1-based indexing
                   os << (i+1) << ' ' << (j+1) << "  " << c << '\n';
                 }
             }
         }
 
       std::vector<numeric_index_type> ibuf, jbuf;
       std::vector<T> cbuf;
       for (auto p : IntRange<processor_id_type>(1, this->n_processors()))
         {
           this->comm().receive(p, ibuf);
           this->comm().receive(p, jbuf);
           this->comm().receive(p, cbuf);
           libmesh_assert_equal_to (ibuf.size(), jbuf.size());
           libmesh_assert_equal_to (ibuf.size(), cbuf.size());
 
           for (auto n : index_range(ibuf))
             os << ibuf[n] << ' ' << jbuf[n] << "  " << cbuf[n] << '\n';
         }
 
       os << "];\n" << "Mat_sparse = spconvert(zzz);" << std::endl;
     }
   else
     {
       std::vector<numeric_index_type> ibuf, jbuf;
       std::vector<T> cbuf;
       std::size_t my_nonzeros = 0;
 
       // We'll assume each processor has access to entire
       // matrix rows, so (*this)(i,j) is valid if i is a local index.
       for (numeric_index_type i : make_range(first_dof, end_dof))
         {
           for (auto j : make_range(this->n()))
             {
               T c = (*this)(i,j);
               if (c != static_cast<T>(0.0))
                 {
                   ibuf.push_back(i);
                   jbuf.push_back(j);
                   cbuf.push_back(c);
                   ++my_nonzeros;
                 }
             }
         }
       this->comm().send(0,my_nonzeros);
       this->comm().send(0,ibuf);
       this->comm().send(0,jbuf);
       this->comm().send(0,cbuf);
     }
 }

◆ print_personal()

template<typename T>

virtual void libMesh::SparseMatrix< T >::print_personal ( std::ostream & os = libMesh::out ) const

pure virtualinherited

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

Implemented in libMesh::StaticCondensation, libMesh::PetscMatrix< T >, libMesh::EpetraMatrix< T >, libMesh::LaspackMatrix< T >, libMesh::DiagonalMatrix< T >, libMesh::EigenSparseMatrix< T >, libMesh::StaticCondensation, libMesh::PetscMFFDMatrix< T >, and libMesh::PetscMFFDMatrix< Number >.

◆ print_petsc_binary()

template<typename T >

void libMesh::SparseMatrix< T >::print_petsc_binary ( const std::string & filename )

virtualinherited

Write the contents of the matrix to a file in PETSc's binary sparse matrix format.

Reimplemented in libMesh::PetscMatrix< T >.

Definition at line 493 of file sparse_matrix.C.

 {
   libmesh_not_implemented_msg
     ("libMesh cannot write PETSc binary-format files from non-PETSc matrices");
 }

◆ print_petsc_hdf5()

template<typename T >

void libMesh::SparseMatrix< T >::print_petsc_hdf5 ( const std::string & filename )

virtualinherited

Write the contents of the matrix to a file in PETSc's HDF5 sparse matrix format.

Reimplemented in libMesh::PetscMatrix< T >.

Definition at line 502 of file sparse_matrix.C.

 {
   libmesh_not_implemented_msg
     ("libMesh cannot write PETSc HDF5-format files from non-PETSc matrices");
 }

◆ processor_id()

processor_id_type libMesh::ParallelObject::processor_id ( ) const

inlineinherited

Returns: The rank of this processor in the group.

Definition at line 114 of file parallel_object.h.

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

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

TIMPI::Communicator::rank

processor_id_type rank() const

libMesh::ParallelObject::_communicator

const Parallel::Communicator & _communicator

Definition: parallel_object.h:120

◆ read()

template<typename T >

void libMesh::SparseMatrix< T >::read ( const std::string & filename )

virtualinherited

Read the contents of the matrix from a file, with the file format inferred from the extension of filename.

Definition at line 511 of file sparse_matrix.C.

 {
   {
     std::ifstream in (filename.c_str());
     libmesh_error_msg_if
       (!in.good(), "ERROR: cannot read file:\n\t" <<
        filename);
   }
 
   std::string_view basename = Utility::basename_of(filename);
 
   const bool gzipped_file = (basename.rfind(".gz") == basename.size() - 3);
 
   if (gzipped_file)
     basename.remove_suffix(3);
 
   if (basename.rfind(".matlab") == basename.size() - 7 ||
       basename.rfind(".m") == basename.size() - 2)
     this->read_matlab(filename);
   else if (basename.rfind(".petsc64") == basename.size() - 8)
     {
 #ifndef LIBMESH_HAVE_PETSC
       libmesh_error_msg("Cannot load PETSc matrix file " <<
                         filename << " without PETSc-enabled libMesh.");
 #endif
 #if LIBMESH_DOF_ID_BYTES != 8
       libmesh_error_msg("Cannot load 64-bit PETSc matrix file " <<
                         filename << " with non-64-bit libMesh.");
 #endif
       this->read_petsc_binary(filename);
     }
   else if (basename.rfind(".petsc32") == basename.size() - 8)
     {
 #ifndef LIBMESH_HAVE_PETSC
       libmesh_error_msg("Cannot load PETSc matrix file " <<
                         filename << " without PETSc-enabled libMesh.");
 #endif
 #if LIBMESH_DOF_ID_BYTES != 4
       libmesh_error_msg("Cannot load 32-bit PETSc matrix file " <<
                         filename << " with non-32-bit libMesh.");
 #endif
       this->read_petsc_binary(filename);
     }
   else
     libmesh_error_msg(" ERROR: Unrecognized matrix file extension on: "
                       << basename
                       << "\n   I understand the following:\n\n"
                       << "     *.matlab  -- Matlab sparse matrix format\n"
                       << "     *.m       -- Matlab sparse matrix format\n"
                       << "     *.petsc32 -- PETSc binary format, 32-bit\n"
                       << "     *.petsc64 -- PETSc binary format, 64-bit\n"
                      );
 }

◆ read_matlab()

template<typename T >

void libMesh::SparseMatrix< T >::read_matlab ( const std::string & filename )

virtualinherited

Read the contents of the matrix from the Matlab-script sparse matrix format used by PETSc.

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 567 of file sparse_matrix.C.

Referenced by ConstraintOperatorTest::test1DCoarseningNewNodes().

 {
   LOG_SCOPE("read_matlab()", "SparseMatrix");
 
 #ifndef LIBMESH_HAVE_CXX11_REGEX
   libmesh_not_implemented();  // What is your compiler?!?  Email us!
   libmesh_ignore(filename);
 #else
   parallel_object_only();
 
   const bool gzipped_file = (filename.rfind(".gz") == filename.size() - 3);
 
   // The sizes we get from the file
   std::size_t m = 0,
               n = 0;
 
   // If we don't already have this size, we'll need to reinit, and
   // determine which rows+columns each processor is in charge of.
   std::vector<numeric_index_type> new_row_starts, new_row_stops,
                                   new_col_starts, new_col_stops;
 
   numeric_index_type new_row_start, new_row_stop,
                      new_col_start, new_col_stop;
 
   // We'll read through the file three times: once to get a reliable
   // value for the matrix size (so we can divvy it up among
   // processors), then again to get the sparsity to send to each
   // processor, then a final time to get the entries to send to each
   // processor.
   //
   // We'll use an istream here; it might be an ifstream if we're
   // opening a raw ASCII file or a gzstream if we're opening a
   // compressed one.
   std::unique_ptr<std::istream> file;
 
   // We'll need a temporary structure to cache matrix entries, because
   // we need to read through the whole file before we know the size
   // and sparsity structure with which we can init().
   //
   // Reading through the file three times via `seekg` doesn't work
   // with our gzstream wrapper, and seems to take three times as long
   // even with a plain ifstream.  What happened to disk caching!?
   std::vector<std::tuple<numeric_index_type, numeric_index_type, T>> entries;
 
   // First read through the file, saving size and entry data
   {
   // We'll read the matrix on processor 0 rather than try to juggle
   // parallel I/O.
   if (this->processor_id() == 0)
     {
       // We'll be using regular expressions to make ourselves slightly
       // more robust to formatting.
       const std::regex start_regex // assignment like "zzz = ["
         ("\\s*\\w+\\s*=\\s*\\[");
       const std::regex end_regex // end of assignment
         ("^[^%]*\\]");
 
       if (gzipped_file)
         {
 #ifdef LIBMESH_HAVE_GZSTREAM
           auto inf = std::make_unique<igzstream>();
           libmesh_assert(inf);
           inf->open(filename.c_str(), std::ios::in);
           file = std::move(inf);
 #else
           libmesh_error_msg("ERROR: need gzstream to handle .gz files!!!");
 #endif
         }
       else
         {
           auto inf = std::make_unique<std::ifstream>();
           libmesh_assert(inf);
 
           std::string new_name = Utility::unzip_file(filename);
 
           inf->open(new_name.c_str(), std::ios::in);
           file = std::move(inf);
         }
 
       // If we have a matrix with all-zero trailing rows, the only
       // way to get the size is if it ended up in a comment
       const std::regex size_regex // comment like "% size = 8 8"
         ("%\\s*[Ss][Ii][Zz][Ee]\\s*=\\s*(\\d+)\\s+(\\d+)");
       const std::string whitespace = " \t";
 
       bool have_started = false;
       bool have_ended = false;
       std::size_t largest_i_seen = 0, largest_j_seen = 0;
 
       // Data for the row we're working on
       // Use 1-based indexing for current_row, as in the file
       std::size_t current_row = 1;
 
       for (std::string line; std::getline(*file, line);)
         {
           std::smatch sm;
 
           // First, try to match an entry.  This is the most common
           // case so we won't rely on slow std::regex for it.
           // stringstream is at least an improvement over that.
 
           // Look for row/col/val like "1 1 -2.0e-4"
 
           std::istringstream l(line);
 
           std::size_t i, j;
           T value;
 
           l >> i >> j >> value;
 
           if (!l.fail())
             {
               libmesh_error_msg_if
                 (!have_started, "Confused by premature entries in matrix file " << filename);
 
               entries.emplace_back(cast_int<numeric_index_type>(i),
                                    cast_int<numeric_index_type>(j),
                                    value);
 
               libmesh_error_msg_if
                 (!i || !j, "Expected 1-based indexing in matrix file "
                  << filename);
 
               current_row = std::max(current_row, i);
 
               libmesh_error_msg_if
                 (i < current_row,
                  "Can't handle out-of-order entries in matrix file "
                  << filename);
 
               largest_i_seen = std::max(i, largest_i_seen);
               largest_j_seen = std::max(j, largest_j_seen);
             }
 
           else if (std::regex_search(line, sm, size_regex))
             {
               const std::string msize = sm[1];
               const std::string nsize = sm[2];
               m = std::stoull(msize);
               n = std::stoull(nsize);
             }
 
           else if (std::regex_search(line, start_regex))
             have_started = true;
 
           else if (std::regex_search(line, end_regex))
             {
               have_ended = true;
               break;
             }
         }
 
       libmesh_error_msg_if
         (!have_started, "Confused by missing assignment beginning in matrix file " << filename);
 
       libmesh_error_msg_if
         (!have_ended, "Confused by missing assignment ending in matrix file " << filename);
 
       libmesh_error_msg_if
         (m > largest_i_seen, "Confused by missing final row(s) in matrix file " << filename);
 
       libmesh_error_msg_if
         (m > 0 && m < largest_i_seen, "Confused by extra final row(s) in matrix file " << filename);
 
       if (!m)
         m = largest_i_seen;
 
       libmesh_error_msg_if
         (n > largest_j_seen, "Confused by missing final column(s) in matrix file " << filename);
 
       libmesh_error_msg_if
         (n > 0 && n < largest_j_seen, "Confused by extra final column(s) in matrix file " << filename);
 
       if (!n)
         n = largest_j_seen;
 
       this->comm().broadcast(m);
       this->comm().broadcast(n);
     }
   else
     {
       this->comm().broadcast(m);
       this->comm().broadcast(n);
     }
 
   if (this->initialized() &&
       m == this->m() &&
       n == this->n())
     {
       new_row_start = this->row_start(),
       new_row_stop  = this->row_stop();
 
       new_col_start = this->col_start(),
       new_col_stop  = this->col_stop();
     }
   else
     {
       // Determine which rows/columns each processor will be in charge of
       new_row_start =     this->processor_id() * m / this->n_processors(),
       new_row_stop  = (this->processor_id()+1) * m / this->n_processors();
 
       new_col_start =     this->processor_id() * n / this->n_processors(),
       new_col_stop  = (this->processor_id()+1) * n / this->n_processors();
     }
 
   this->comm().gather(0, new_row_start, new_row_starts);
   this->comm().gather(0, new_row_stop, new_row_stops);
   this->comm().gather(0, new_col_start, new_col_starts);
   this->comm().gather(0, new_col_stop, new_col_stops);
 
   } // Done reading entry data and broadcasting matrix size
 
   // Calculate the matrix sparsity and initialize it second
   {
   // Deduce the sparsity pattern, or at least the maximum number of
   // on- and off- diagonal non-zeros per row.
   numeric_index_type  on_diagonal_nonzeros =0,
                      off_diagonal_nonzeros =0;
 
   if (this->processor_id() == 0)
     {
       // Data for the row we're working on
       // Use 1-based indexing for current_row, as in the file
       numeric_index_type current_row = 1;
       processor_id_type current_proc = 0;
       numeric_index_type current_on_diagonal_nonzeros = 0;
       numeric_index_type current_off_diagonal_nonzeros = 0;
 
       for (auto [i, j, value] : entries)
         {
           if (i > current_row)
             {
               current_row = i;
               // +1 for 1-based indexing in file
               while (current_row >= (new_row_stops[current_proc]+1))
                 ++current_proc;
               current_on_diagonal_nonzeros = 0;
               current_off_diagonal_nonzeros = 0;
             }
 
           // +1 for 1-based indexing in file
           if (j >= (new_col_starts[current_proc]+1) &&
               j < (new_col_stops[current_proc]+1))
             {
               ++current_on_diagonal_nonzeros;
               on_diagonal_nonzeros =
                 std::max(on_diagonal_nonzeros,
                          current_on_diagonal_nonzeros);
             }
           else
             {
               ++current_off_diagonal_nonzeros;
               off_diagonal_nonzeros =
                 std::max(off_diagonal_nonzeros,
                          current_off_diagonal_nonzeros);
             }
         }
     }
 
   this->comm().broadcast(on_diagonal_nonzeros);
   this->comm().broadcast(off_diagonal_nonzeros);
 
   this->init(m, n,
              new_row_stop-new_row_start,
              new_col_stop-new_col_start,
              on_diagonal_nonzeros,
              off_diagonal_nonzeros);
   }
 
   // Set the matrix values last.
   // Convert from 1-based to 0-based indexing
   if (this->processor_id() == 0)
     for (auto [i, j, value] : entries)
       this->set(i-1, j-1, value);
 
   this->close();
 #endif
 }

◆ read_petsc_binary()

template<typename T >

void libMesh::SparseMatrix< T >::read_petsc_binary ( const std::string & filename )

virtualinherited

Read the contents of the matrix from a file in PETSc's binary sparse matrix format.

Reimplemented in libMesh::PetscMatrix< T >.

Definition at line 849 of file sparse_matrix.C.

 {
   libmesh_not_implemented_msg
     ("libMesh cannot read PETSc binary-format files into non-PETSc matrices");
 }

◆ read_petsc_hdf5()

template<typename T >

void libMesh::SparseMatrix< T >::read_petsc_hdf5 ( const std::string & filename )

virtualinherited

Read the contents of the matrix from a file in PETSc's HDF5 sparse matrix format.

Reimplemented in libMesh::PetscMatrix< T >.

Definition at line 858 of file sparse_matrix.C.

 {
   libmesh_not_implemented_msg
     ("libMesh cannot read PETSc HDF5-format files into non-PETSc matrices");
 }

◆ reinit_submatrix()

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 540 of file sparse_matrix.h.

   {
     this->_get_submatrix(submatrix,
                          rows,
                          cols,
                          true); // true means REUSE submatrix
   }

◆ require_sparsity_pattern()

template<typename T>

virtual bool libMesh::PetscMatrixShellMatrix< T >::require_sparsity_pattern ( ) const

inlineoverridevirtual

Returns: Whether this matrix needs the sparsity pattern computed by the DofMap

Reimplemented from libMesh::SparseMatrix< T >.

Reimplemented in libMesh::StaticCondensation.

Definition at line 59 of file petsc_matrix_shell_matrix.h.

59 { return false; }

◆ restore_original_nonzero_pattern()

template<typename T>

virtual void libMesh::SparseMatrix< T >::restore_original_nonzero_pattern ( )

inlinevirtualinherited

Reset the memory storage of the matrix.

Unlike clear(), this does not destroy the matrix but rather will reset the matrix to use the original preallocation or when using hash table matrix assembly (see use_hash_table()) will reset (clear) the hash table used for assembly. In the words of the MatResetPreallocation documentation in PETSc, 'current values in the matrix are lost in this call', so a user can expect to have back their original sparsity pattern in a zeroed state

Reimplemented in libMesh::PetscMatrix< T >, and libMesh::DiagonalMatrix< T >.

Definition at line 619 of file sparse_matrix.h.

619 { libmesh_not_implemented(); }

◆ row_start()

template<typename T >

numeric_index_type libMesh::PetscMatrixBase< T >::row_start ( ) const

overridevirtualinherited

Returns: The index of the first matrix row stored on this processor.

Implements libMesh::SparseMatrix< T >.

Reimplemented in libMesh::StaticCondensation, and libMesh::StaticCondensation.

Definition at line 178 of file petsc_matrix_base.C.

 {
   libmesh_assert (this->initialized());
 
   PetscInt start=0, stop=0;
 
   LibmeshPetscCall(MatGetOwnershipRange(this->_mat, &start, &stop));
 
   return static_cast<numeric_index_type>(start);
 }

◆ row_stop()

template<typename T >

numeric_index_type libMesh::PetscMatrixBase< T >::row_stop ( ) const

overridevirtualinherited

Returns: The index of the last matrix row (+1) stored on this processor.

Implements libMesh::SparseMatrix< T >.

Reimplemented in libMesh::StaticCondensation, and libMesh::StaticCondensation.

Definition at line 190 of file petsc_matrix_base.C.

 {
   libmesh_assert (this->initialized());
 
   PetscInt start=0, stop=0;
 
   LibmeshPetscCall(MatGetOwnershipRange(this->_mat, &start, &stop));
 
   return static_cast<numeric_index_type>(stop);
 }

◆ scale()

template<typename T>

void libMesh::SparseMatrix< T >::scale ( const T scale )

virtualinherited

Scales all elements of this matrix by scale.

Reimplemented in libMesh::PetscMatrix< T >.

Definition at line 867 of file sparse_matrix.C.

 {
   libmesh_assert(this->closed());
 
   for (const auto i : make_range(this->row_start(), this->row_stop()))
     for (const auto j : make_range(this->col_start(), this->col_stop()))
       this->set(i, j, (*this)(i, j) * scale);
 }

◆ set()

template<typename T>

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

pure virtualinherited

Set the element (i,j) to value.

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

Implemented in libMesh::StaticCondensation, libMesh::PetscMatrix< T >, libMesh::EpetraMatrix< T >, libMesh::DiagonalMatrix< T >, libMesh::LaspackMatrix< T >, libMesh::EigenSparseMatrix< T >, libMesh::StaticCondensation, libMesh::PetscMFFDMatrix< T >, libMesh::PetscMFFDMatrix< Number >, and libMesh::LumpedMassMatrix< T >.

Referenced by AssembleOptimization::equality_constraints_jacobian(), AssembleOptimization::inequality_constraints_jacobian(), libMesh::MatrixFillAction< ValIn, ValOut >::insert(), libMesh::System::projection_matrix(), ConstraintOperatorTest::test1DCoarseningOperator(), SystemsTest::testProjectMatrix1D(), SystemsTest::testProjectMatrix2D(), and SystemsTest::testProjectMatrix3D().

◆ set_context()

template<typename T >

void libMesh::PetscMatrixBase< T >::set_context ( )

inherited

Set the context (ourself) for _mat.

Definition at line 105 of file petsc_matrix_base.C.

 {
   libmesh_assert(this->_mat);
   PetscContainer container;
   LibmeshPetscCall(PetscContainerCreate(this->comm().get(), &container));
   LibmeshPetscCall(PetscContainerSetPointer(container, this));
   LibmeshPetscCall(PetscObjectCompose((PetscObject)(Mat)this->_mat, "PetscMatrixCtx", (PetscObject)container));
   LibmeshPetscCall(PetscContainerDestroy(&container));
 }

◆ set_destroy_mat_on_exit()

template<typename T >

void libMesh::PetscMatrixBase< T >::set_destroy_mat_on_exit ( bool destroy = true )

inherited

If set to false, we don't delete the Mat on destruction and allow instead for PETSc to manage it.

Definition at line 91 of file petsc_matrix_base.C.

 {
   this->_destroy_mat_on_exit = destroy;
 }

◆ solver_package()

template<typename T>

virtual SolverPackage libMesh::PetscMatrixBase< T >::solver_package ( )

inlineoverridevirtualinherited

Implements libMesh::SparseMatrix< T >.

Reimplemented in libMesh::StaticCondensation, and libMesh::StaticCondensation.

Definition at line 107 of file petsc_matrix_base.h.

   {
     return PETSC_SOLVERS;
   }

◆ supports_hash_table()

template<typename T>

virtual bool libMesh::SparseMatrix< T >::supports_hash_table ( ) const

inlinevirtualinherited

Returns: Whether the matrix supports hash table assembly

Reimplemented in libMesh::PetscMatrix< T >.

Definition at line 594 of file sparse_matrix.h.

594 { return false; }

◆ swap()

template<typename T>

void libMesh::PetscMatrixBase< T >::swap ( PetscMatrixBase< T > & m_in )

inherited

Swaps the internal data pointers of two PetscMatrices, no actual values are swapped.

Definition at line 98 of file petsc_matrix_base.C.

Referenced by DMlibMeshJacobian().

 {
   std::swap(_mat, m_in._mat);
   std::swap(_destroy_mat_on_exit, m_in._destroy_mat_on_exit);
 }

◆ update_sparsity_pattern()

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 175 of file sparse_matrix.h.

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

175 {}

◆ use_hash_table() [1/2]

template<typename T >

void libMesh::SparseMatrix< T >::use_hash_table ( bool use_hash )

inherited

Sets whether to use hash table assembly.

This will error if the passed-in value is true and the matrix type does not support hash tables. Hash table or hash map assembly means storing maps from i-j locations in the matrix to values. Because it is a hash map as opposed to a contiguous array of data, no preallocation is required to use it

Definition at line 667 of file sparse_matrix.h.

Referenced by PetscMatrixTest::testPetscCopyFromHash().

 {
   libmesh_error_msg_if(use_hash && !this->supports_hash_table(),
                        "This matrix class does not support hash table assembly");
   this->_use_hash_table = use_hash;
 }

◆ use_hash_table() [2/2]

template<typename T>

bool libMesh::SparseMatrix< T >::use_hash_table ( ) const

inlineinherited

Returns: Whether this matrix is using hash table assembly. Hash table or hash map assembly means storing maps from i-j locations in the matrix to values. Because it is a hash map as opposed to a contiguous array of data, no preallocation is required to use it

Definition at line 609 of file sparse_matrix.h.

Referenced by libMesh::SparseMatrix< ValOut >::require_sparsity_pattern().

609 { return _use_hash_table; }

libMesh::SparseMatrix::_use_hash_table

bool _use_hash_table

Flag indicating whether the matrix is assembled using a hash table.

Definition: sparse_matrix.h:658

◆ vector_mult()

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 209 of file sparse_matrix.C.

 {
   dest.zero();
   this->vector_mult_add(dest,arg);
 }

◆ vector_mult_add()

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 219 of file sparse_matrix.C.

Referenced by libMesh::ImplicitSystem::weighted_sensitivity_adjoint_solve().

 {
   /* This functionality is actually implemented in the \p
      NumericVector class.  */
   dest.add_vector(arg,*this);
 }

◆ zero()

template<typename T>

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

pure virtualinherited

Set all entries to 0.

Implemented in libMesh::StaticCondensation, libMesh::PetscMatrix< T >, libMesh::EpetraMatrix< T >, libMesh::DiagonalMatrix< T >, libMesh::LaspackMatrix< T >, libMesh::EigenSparseMatrix< T >, libMesh::StaticCondensation, libMesh::PetscMFFDMatrix< T >, and libMesh::PetscMFFDMatrix< Number >.

Referenced by add_M_C_K_helmholtz(), libMesh::RBSCMConstruction::Aq_inner_product(), libMesh::ImplicitSystem::assemble(), AssembleOptimization::assemble_A_and_F(), libMesh::RBConstruction::assemble_Aq_matrix(), libMesh::RBConstruction::assemble_inner_product_matrix(), libMesh::TransientRBConstruction::assemble_L2_matrix(), libMesh::TransientRBConstruction::assemble_mass_matrix(), libMesh::TransientRBConstruction::assemble_Mq_matrix(), libMesh::FEMSystem::assembly(), libMesh::NewmarkSystem::compute_matrix(), libMesh::RBConstruction::compute_residual_dual_norm_slow(), libMesh::RBSCMConstruction::compute_SCM_bounding_box(), DMlibMeshJacobian(), AssembleOptimization::equality_constraints_jacobian(), libMesh::RBSCMConstruction::evaluate_stability_constant(), AssembleOptimization::hessian(), AssembleOptimization::inequality_constraints_jacobian(), LargeDeformationElasticity::jacobian(), libMesh::libmesh_petsc_snes_jacobian(), libMesh::libmesh_petsc_snes_residual(), libMesh::RBSCMConstruction::load_matrix_B(), main(), LinearElasticityWithContact::residual_and_jacobian(), libMesh::ClawSystem::solve_conservation_law(), libMesh::TransientRBConstruction::truth_assembly(), and libMesh::RBConstruction::truth_assembly().

◆ zero_clone()

template<typename T>

virtual std::unique_ptr<SparseMatrix<T> > libMesh::SparseMatrix< T >::zero_clone ( ) const

pure virtualinherited

Returns: A smart pointer to a copy of this matrix with the same type, size, and partitioning, but with all zero entries.

Note: This must be overridden in the derived classes.

Implemented in libMesh::StaticCondensation, libMesh::PetscMatrix< T >, libMesh::EpetraMatrix< T >, libMesh::DiagonalMatrix< T >, libMesh::LaspackMatrix< T >, libMesh::EigenSparseMatrix< T >, libMesh::StaticCondensation, libMesh::PetscMFFDMatrix< T >, libMesh::PetscMFFDMatrix< Number >, and libMesh::LumpedMassMatrix< T >.

◆ zero_rows()

template<typename T>

void libMesh::SparseMatrix< T >::zero_rows	(	std::vector< numeric_index_type > &	rows,
		T	diag_value = `0.0`
	)

virtualinherited

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

Reimplemented in libMesh::DiagonalMatrix< T >, and libMesh::PetscMatrix< T >.

Definition at line 230 of file sparse_matrix.C.

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

Friends And Related Function Documentation

◆ init_shell_mat [1/2]

template<typename T>

void init_shell_mat ( PetscMatrixShellMatrix< T > & obj )

friend

◆ init_shell_mat [2/2]

template<typename T>

void init_shell_mat	(	PetscMatrixShellMatrix< T > &	obj,
		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	blocksize_in
	)

friend

Member Data Documentation

◆ _communicator

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

protectedinherited

Definition at line 120 of file parallel_object.h.

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

◆ _counts

ReferenceCounter::Counts libMesh::ReferenceCounter::_counts

staticprotectedinherited

Actually holds the data.

Definition at line 124 of file reference_counter.h.

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

◆ _destroy_mat_on_exit

template<typename T>

bool libMesh::PetscMatrixBase< T >::_destroy_mat_on_exit

protectedinherited

This boolean value should only be set to false for the constructor which takes a PETSc Mat object.

Definition at line 186 of file petsc_matrix_base.h.

Referenced by libMesh::PetscMatrixBase< Number >::swap().

◆ _dof_map

template<typename T>

DofMap const* libMesh::SparseMatrix< T >::_dof_map

protectedinherited

The DofMap object associated with this object.

May be queried for degree-of-freedom counts on processors.

Definition at line 641 of file sparse_matrix.h.

◆ _enable_print_counter

bool libMesh::ReferenceCounter::_enable_print_counter = true

staticprotectedinherited

Flag to control whether reference count information is printed when print_info is called.

Definition at line 143 of file reference_counter.h.

Referenced by libMesh::ReferenceCounter::disable_print_counter_info(), libMesh::ReferenceCounter::enable_print_counter_info(), and libMesh::ReferenceCounter::print_info().

◆ _is_initialized

template<typename T>

bool libMesh::SparseMatrix< T >::_is_initialized

protectedinherited

Flag indicating whether or not the matrix has been initialized.

Definition at line 653 of file sparse_matrix.h.

Referenced by libMesh::PetscMatrix< T >::_get_submatrix(), libMesh::PetscMatrix< T >::create_submatrix_nosort(), libMesh::EpetraMatrix< T >::EpetraMatrix(), libMesh::PetscMatrix< T >::get_transpose(), and libMesh::SparseMatrix< ValOut >::initialized().

◆ _mat

template<typename T>

Mat libMesh::PetscMatrixBase< T >::_mat

protectedinherited

PETSc matrix datatype to store values.

Definition at line 180 of file petsc_matrix_base.h.

Referenced by libMesh::PetscMatrix< T >::_get_submatrix(), libMesh::PetscMatrix< T >::add(), libMesh::PetscMatrix< T >::create_submatrix_nosort(), libMesh::PetscMatrix< T >::get_transpose(), libMesh::PetscMatrixBase< Number >::mat(), libMesh::PetscMatrix< T >::operator=(), and libMesh::PetscMatrixBase< Number >::swap().

◆ _mutex

Threads::spin_mutex libMesh::ReferenceCounter::_mutex

staticprotectedinherited

Mutual exclusion object to enable thread-safe reference counting.

Definition at line 137 of file reference_counter.h.

◆ _n_objects

Threads::atomic< unsigned int > libMesh::ReferenceCounter::_n_objects

staticprotectedinherited

The number of objects.

Print the reference count information when the number returns to 0.

Definition at line 132 of file reference_counter.h.

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

◆ _omit_constrained_dofs

template<typename T>

const bool libMesh::PetscMatrixShellMatrix< T >::_omit_constrained_dofs

private

Whether to omit constrained degrees of freedom.

Definition at line 67 of file petsc_matrix_shell_matrix.h.

◆ _sp

template<typename T>

SparsityPattern::Build const* libMesh::SparseMatrix< T >::_sp

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 648 of file sparse_matrix.h.

◆ _use_hash_table

template<typename T>

bool libMesh::SparseMatrix< T >::_use_hash_table

protectedinherited

Flag indicating whether the matrix is assembled using a hash table.

Definition at line 658 of file sparse_matrix.h.

Referenced by libMesh::SparseMatrix< ValOut >::use_hash_table().

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

include/numerics/petsc_matrix_shell_matrix.h
src/numerics/petsc_matrix_shell_matrix.C

Public Member Functions

Static Public Member Functions

Protected Types

Protected Member Functions

Protected Attributes

Static Protected Attributes

Private Attributes

Friends

Detailed Description

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

Member Typedef Documentation

◆ Counts

Constructor & Destructor Documentation

◆ PetscMatrixShellMatrix()

Member Function Documentation

◆ _get_submatrix()

◆ add() [1/2]

◆ add() [2/2]

◆ add_block_matrix() [1/2]

◆ add_block_matrix() [2/2]

◆ add_matrix() [1/2]

◆ add_matrix() [2/2]

◆ add_sparse_matrix()

◆ attach_dof_map()

◆ attach_sparsity_pattern()

◆ build()

◆ clear()

◆ clone()

◆ close()

◆ closed()

◆ col_start()

◆ col_stop()

◆ comm()

◆ create_submatrix()

◆ create_submatrix_nosort()

◆ disable_print_counter_info()

◆ enable_print_counter_info()

◆ flush()

◆ get_context()

◆ get_diagonal()

◆ get_info()

◆ get_row()

◆ get_transpose()

◆ increment_constructor_count()

◆ increment_destructor_count()

◆ init() [1/2]

◆ init() [2/2]

◆ initialized()

◆ l1_norm()

◆ l1_norm_diff()

◆ linfty_norm()

◆ local_m()

◆ local_n()

◆ m()

◆ mat() [1/2]

◆ mat() [2/2]

◆ matrix_matrix_mult()

◆ n()

◆ n_nonzeros()

◆ n_objects()

◆ n_processors()

◆ need_full_sparsity_pattern()

◆ operator()()

◆ operator=()

◆ print() [1/2]

◆ print() [2/2]

◆ print_info()

◆ print_matlab()

◆ print_personal()

◆ print_petsc_binary()

◆ print_petsc_hdf5()

◆ processor_id()

◆ read()

◆ read_matlab()

◆ read_petsc_binary()

◆ read_petsc_hdf5()

◆ reinit_submatrix()

◆ require_sparsity_pattern()

◆ restore_original_nonzero_pattern()

◆ row_start()

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