This class provides a nice interface to the PETSc C-based data structures for parallel, sparse matrices. More...

#include <petsc_matrix.h>

Inheritance diagram for libMesh::PetscMatrix< T >:

Public Member Functions
	PetscMatrix (const Parallel::Communicator &comm_in)
	Constructor; initializes the matrix to be empty, without any structure, i.e. More...

	PetscMatrix (Mat m, const Parallel::Communicator &comm_in)
	Constructor. More...

	PetscMatrix (PetscMatrix &&)=delete
	This class manages a C-style struct (Mat) manually, so we don't want to allow any automatic copy/move functions to be generated, and we can't default the destructor. More...

	PetscMatrix (const PetscMatrix &)=delete

PetscMatrix &	operator= (const PetscMatrix &)=delete

PetscMatrix &	operator= (PetscMatrix &&)=delete

virtual	~PetscMatrix ()

void	set_matrix_type (PetscMatrixType mat_type)

virtual void	init (const numeric_index_type m, const numeric_index_type n, const numeric_index_type m_l, const numeric_index_type n_l, const numeric_index_type nnz=30, const numeric_index_type noz=10, const numeric_index_type blocksize=1) override
	Initialize SparseMatrix with the specified sizes. More...

void	init (const numeric_index_type m, const numeric_index_type n, const numeric_index_type m_l, const numeric_index_type n_l, const std::vector< numeric_index_type > &n_nz, const std::vector< numeric_index_type > &n_oz, const numeric_index_type blocksize=1)
	Initialize a PETSc matrix. More...

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

void	update_preallocation_and_zero ()
	Update the sparsity pattern based on `dof_map`, and set the matrix to zero. More...

virtual void	clear () override
	Restores the `SparseMatrix<T>` to a pristine state. More...

virtual void	zero () override
	Set all entries to 0. More...

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

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

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

virtual numeric_index_type	m () const override

virtual numeric_index_type	n () const override

virtual numeric_index_type	row_start () const override

virtual numeric_index_type	row_stop () const override

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

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

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

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

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

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

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

virtual T	operator() (const numeric_index_type i, const numeric_index_type j) const override

virtual Real	l1_norm () const override

virtual Real	linfty_norm () const override

virtual bool	closed () const override

virtual void	set_destroy_mat_on_exit (bool destroy=true)
	If set to false, we don't delete the Mat on destruction and allow instead for `PETSc` to manage it. More...

virtual void	print_personal (std::ostream &os=libMesh::out) const override
	Print the contents of the matrix to the screen with the PETSc viewer. More...

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

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

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

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

Mat	mat ()

virtual bool	initialized () const

void	attach_dof_map (const DofMap &dof_map)
	Get a pointer to the `DofMap` to use. More...

virtual bool	need_full_sparsity_pattern () const

virtual void	update_sparsity_pattern (const SparsityPattern::Graph &)
	Updates the matrix sparsity pattern. More...

void	print (std::ostream &os=libMesh::out, const bool sparse=false) const
	Print the contents of the matrix to the screen in a uniform style, regardless of matrix/solver package being used. More...

virtual void	create_submatrix (SparseMatrix< T > &submatrix, const std::vector< numeric_index_type > &rows, const std::vector< numeric_index_type > &cols) const
	This function creates a matrix called "submatrix" which is defined by the row and column indices given in the "rows" and "cols" entries. More...

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

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

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

const Parallel::Communicator &	comm () const

processor_id_type	n_processors () const

processor_id_type	processor_id () const

Static Public Member Functions
static std::unique_ptr< SparseMatrix< T > >	build (const Parallel::Communicator &comm, const SolverPackage solver_package=libMesh::default_solver_package())
	Builds a `SparseMatrix<T>` using the linear solver package specified by `solver_package`. More...

static std::string	get_info ()
	Gets a string containing the reference information. More...

static void	print_info (std::ostream &out=libMesh::out)
	Prints the reference information, by default to `libMesh::out`. More...

static unsigned int	n_objects ()
	Prints the number of outstanding (created, but not yet destroyed) objects. More...

static void	enable_print_counter_info ()
	Methods to enable/disable the reference counter output from print_info() More...

static void	disable_print_counter_info ()

Protected Types
typedef std::map< std::string, std::pair< unsigned int, unsigned int > >	Counts
	Data structure to log the information. More...

Protected Member Functions
virtual void	_get_submatrix (SparseMatrix< T > &submatrix, const std::vector< numeric_index_type > &rows, const std::vector< numeric_index_type > &cols, const bool reuse_submatrix) const override
	This function either creates or re-initializes a matrix called `submatrix` which is defined by the indices given in the `rows` and `cols` vectors. More...

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

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

Protected Attributes
DofMap const *	_dof_map
	The `DofMap` object associated with this object. More...

bool	_is_initialized
	Flag indicating whether or not the matrix has been initialized. More...

const Parallel::Communicator &	_communicator

Static Protected Attributes
static Counts	_counts
	Actually holds the data. More...

static Threads::atomic< unsigned int >	_n_objects
	The number of objects. More...

static Threads::spin_mutex	_mutex
	Mutual exclusion object to enable thread-safe reference counting. More...

static bool	_enable_print_counter
	Flag to control whether reference count information is printed when print_info is called. More...

Private Attributes
Mat	_mat
	PETSc matrix datatype to store values. More...

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

PetscMatrixType	_mat_type

Detailed Description

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

This class provides a nice interface to the PETSc C-based data structures for parallel, sparse matrices.

All overridden virtual functions are documented in sparse_matrix.h.

Author: Benjamin S. Kirk

Date: 2002 SparseMatrix interface to PETSc Mat.

Definition at line 78 of file petsc_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 117 of file reference_counter.h.

Constructor & Destructor Documentation

◆ PetscMatrix() [1/4]

template<typename T>

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

explicit

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

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

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

◆ PetscMatrix() [2/4]

template<typename T>

libMesh::PetscMatrix< T >::PetscMatrix	(	Mat	m,
		const Parallel::Communicator &	comm_in
	)

explicit

Constructor.

Creates a PetscMatrix assuming you already have a valid Mat object. In this case, m is NOT destroyed by the PetscMatrix destructor when this object goes out of scope. This allows ownership of m to remain with the original creator, and to simply provide additional functionality with the PetscMatrix.

◆ PetscMatrix() [3/4]

template<typename T>

libMesh::PetscMatrix< T >::PetscMatrix ( PetscMatrix< T > && )

delete

This class manages a C-style struct (Mat) manually, so we don't want to allow any automatic copy/move functions to be generated, and we can't default the destructor.

◆ PetscMatrix() [4/4]

template<typename T>

libMesh::PetscMatrix< T >::PetscMatrix ( const PetscMatrix< T > & )

delete

◆ ~PetscMatrix()

template<typename T>

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

virtual

Member Function Documentation

◆ _get_submatrix()

template<typename T>

virtual void libMesh::PetscMatrix< T >::_get_submatrix	(	SparseMatrix< T > &	submatrix,
		const std::vector< numeric_index_type > &	rows,
		const std::vector< numeric_index_type > &	cols,
		const bool	reuse_submatrix
	)		const

overrideprotectedvirtual

This function either creates or re-initializes a matrix called submatrix which is defined by the indices given in the rows and cols vectors.

This function is implemented in terms of MatGetSubMatrix(). The reuse_submatrix parameter determines whether or not PETSc will treat submatrix as one which has already been used (had memory allocated) or as a new matrix.

Reimplemented from libMesh::SparseMatrix< T >.

◆ add() [1/2]

template<typename T>

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

overridevirtual

Add value to the element (i,j).

Throws an error if the entry does not exist. Zero values can be "added" to non-existent entries.

Implements libMesh::SparseMatrix< T >.

◆ add() [2/2]

template<typename T>

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

overridevirtual

Compute A += a*X for scalar a, matrix X.

Note: The matrices A and X need to have the same nonzero pattern, otherwise PETSc will crash!; It is advisable to not only allocate appropriate memory with init(), but also explicitly zero the terms of this whenever you add a non-zero value to X.; X will be closed, if not already done, before performing any work.

Implements libMesh::SparseMatrix< T >.

◆ add_block_matrix() [1/2]

template<typename T>

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

overridevirtual

Add the full matrix dm to the SparseMatrix.

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

Reimplemented from libMesh::SparseMatrix< T >.

Referenced by libMesh::PetscMatrix< libMesh::Real >::add_block_matrix().

◆ add_block_matrix() [2/2]

template<typename T>

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

overridevirtual

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

Thus the matrix dm must be square.

Reimplemented from libMesh::SparseMatrix< T >.

Definition at line 191 of file petsc_matrix.h.

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

libMesh::PetscMatrix::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) override

Add the full matrix dm to the SparseMatrix.

◆ add_matrix() [1/2]

template<typename T>

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

overridevirtual

Add the full matrix dm to the SparseMatrix.

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

Implements libMesh::SparseMatrix< T >.

◆ add_matrix() [2/2]

template<typename T>

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

overridevirtual

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

Thus the matrix dm must be square.

Implements libMesh::SparseMatrix< T >.

◆ attach_dof_map()

template<typename T>

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

inherited

Get a pointer to the DofMap to use.

Definition at line 109 of file sparse_matrix.h.

110 { _dof_map = &dof_map; }

libMesh::SparseMatrix::_dof_map

DofMap const * _dof_map

The DofMap object associated with this object.

Definition: sparse_matrix.h:425

◆ build()

template<typename T>

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

staticinherited

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

◆ clear()

template<typename T>

virtual void libMesh::PetscMatrix< T >::clear ( )

overridevirtual

Restores the SparseMatrix<T> to a pristine state.

Implements libMesh::SparseMatrix< T >.

◆ close()

template<typename T>

virtual void libMesh::PetscMatrix< T >::close ( )

overridevirtual

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

Implements libMesh::SparseMatrix< T >.

◆ closed()

template<typename T>

virtual bool libMesh::PetscMatrix< T >::closed ( ) const

overridevirtual

Returns: true if the matrix has been assembled.

Implements libMesh::SparseMatrix< T >.

◆ comm()

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

inherited

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

Definition at line 89 of file parallel_object.h.

References libMesh::ParallelObject::_communicator.

Referenced by libMesh::EpetraVector< T >::EpetraVector(), libMesh::Parallel::sync_element_data_by_parent_id(), libMesh::Parallel::sync_node_data_by_element_id(), and libMesh::Parallel::sync_node_data_by_element_id_once().

90 { return _communicator; }

libMesh::ParallelObject::_communicator

const Parallel::Communicator & _communicator

Definition: parallel_object.h:107

◆ 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

virtualinherited

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

Currently this operation is only defined for the PetscMatrix type.

Definition at line 354 of file sparse_matrix.h.

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

◆ disable_print_counter_info()

static void libMesh::ReferenceCounter::disable_print_counter_info ( )

staticinherited

◆ enable_print_counter_info()

static void libMesh::ReferenceCounter::enable_print_counter_info ( )

staticinherited

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

◆ flush()

template<typename T>

virtual void libMesh::PetscMatrix< T >::flush ( )

overridevirtual

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

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

Reimplemented from libMesh::SparseMatrix< T >.

◆ get_diagonal()

template<typename T>

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

overridevirtual

Copies the diagonal part of the matrix into dest.

Implements libMesh::SparseMatrix< T >.

◆ get_info()

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

staticinherited

Gets a string containing the reference information.

◆ get_transpose()

template<typename T>

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

overridevirtual

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

Implements libMesh::SparseMatrix< T >.

◆ increment_constructor_count()

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

protectedinherited

Increments the construction counter.

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

Definition at line 181 of file reference_counter.h.

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

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

 {
   Threads::spin_mutex::scoped_lock lock(Threads::spin_mtx);
   std::pair<unsigned int, unsigned int> & p = _counts[name];
 
   p.first++;
 }

◆ increment_destructor_count()

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

protectedinherited

Increments the destruction counter.

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

Definition at line 194 of file reference_counter.h.

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

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

 {
   Threads::spin_mutex::scoped_lock lock(Threads::spin_mtx);
   std::pair<unsigned int, unsigned int> & p = _counts[name];
 
   p.second++;
 }

◆ init() [1/3]

template<typename T>

virtual void libMesh::PetscMatrix< T >::init	(	const numeric_index_type	m,
		const numeric_index_type	n,
		const numeric_index_type	m_l,
		const numeric_index_type	n_l,
		const 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 >.

◆ init() [2/3]

template<typename T>

void libMesh::PetscMatrix< T >::init	(	const numeric_index_type	m,
		const numeric_index_type	n,
		const numeric_index_type	m_l,
		const numeric_index_type	n_l,
		const std::vector< numeric_index_type > &	n_nz,
		const std::vector< numeric_index_type > &	n_oz,
		const numeric_index_type	blocksize = `1`
	)

Initialize a PETSc matrix.

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.
n_nz	array containing the number of nonzeros in each row of the DIAGONAL portion of the local submatrix.
n_oz	Array containing the number of nonzeros in each row of the OFF-DIAGONAL portion of the local submatrix.
blocksize	Optional value indicating dense coupled blocks for systems with multiple variables all of the same type.

◆ init() [3/3]

template<typename T>

virtual void libMesh::PetscMatrix< T >::init ( )

overridevirtual

Initialize this matrix using the sparsity structure computed by dof_map.

Implements libMesh::SparseMatrix< T >.

◆ initialized()

template<typename T>

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

virtualinherited

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

Definition at line 104 of file sparse_matrix.h.

104 { return _is_initialized; }

libMesh::SparseMatrix::_is_initialized

bool _is_initialized

Flag indicating whether or not the matrix has been initialized.

Definition: sparse_matrix.h:430

◆ l1_norm()

template<typename T>

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

overridevirtual

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

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

Implements libMesh::SparseMatrix< T >.

◆ linfty_norm()

template<typename T>

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

overridevirtual

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

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

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

Implements libMesh::SparseMatrix< T >.

◆ m()

template<typename T>

virtual numeric_index_type libMesh::PetscMatrix< T >::m ( ) const

overridevirtual

Returns: The row-dimension of the matrix.

Implements libMesh::SparseMatrix< T >.

◆ mat()

template<typename T>

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

Returns: The raw PETSc matrix pointer.

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

Definition at line 253 of file petsc_matrix.h.

253 { libmesh_assert (_mat); return _mat; }

libMesh::PetscMatrix::_mat

Mat _mat

PETSc matrix datatype to store values.

Definition: petsc_matrix.h:277

◆ n()

template<typename T>

virtual numeric_index_type libMesh::PetscMatrix< T >::n ( ) const

overridevirtual

Returns: The column-dimension of the matrix.

Implements libMesh::SparseMatrix< T >.

◆ n_objects()

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

staticinherited

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

Definition at line 83 of file reference_counter.h.

References libMesh::ReferenceCounter::_n_objects.

84 { return _n_objects; }

libMesh::ReferenceCounter::_n_objects

static Threads::atomic< unsigned int > _n_objects

The number of objects.

Definition: reference_counter.h:130

◆ n_processors()

processor_id_type libMesh::ParallelObject::n_processors ( ) const

inherited

Returns: The number of processors in the group.

Definition at line 95 of file parallel_object.h.

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

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

96 { return cast_int<processor_id_type>(_communicator.size()); }

libMesh::Parallel::Communicator::size

processor_id_type size() const

Definition: communicator.h:175

libMesh::ParallelObject::_communicator

const Parallel::Communicator & _communicator

Definition: parallel_object.h:107

◆ need_full_sparsity_pattern()

template<typename T>

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

virtualinherited

Returns: true if this sparse matrix format needs to be fed the graph of the sparse matrix.

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

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

Definition at line 121 of file sparse_matrix.h.

122 { return false; }

◆ operator()()

template<typename T>

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

overridevirtual

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

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

Implements libMesh::SparseMatrix< T >.

◆ operator=() [1/2]

template<typename T>

PetscMatrix& libMesh::PetscMatrix< T >::operator= ( const PetscMatrix< T > & )

delete

◆ operator=() [2/2]

template<typename T>

PetscMatrix& libMesh::PetscMatrix< T >::operator= ( PetscMatrix< T > && )

delete

◆ print()

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.

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

◆ print_info()

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

staticinherited

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

◆ print_matlab()

template<typename T>

virtual void libMesh::PetscMatrix< T >::print_matlab ( const std::string & = "" ) const

overridevirtual

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

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

Reimplemented from libMesh::SparseMatrix< T >.

◆ print_personal()

template<typename T>

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

overridevirtual

Print the contents of the matrix to the screen with the PETSc viewer.

This function only allows printing to standard out since we have limited ourselves to one PETSc implementation for writing.

Implements libMesh::SparseMatrix< T >.

◆ processor_id()

processor_id_type libMesh::ParallelObject::processor_id ( ) const

inherited

Returns: The rank of this processor in the group.

Definition at line 101 of file parallel_object.h.

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

Referenced by libMesh::DofMap::end_dof(), libMesh::DofMap::end_old_dof(), libMesh::DofMap::first_dof(), libMesh::DofMap::first_old_dof(), libMesh::DofMap::last_dof(), libMesh::MeshBase::n_active_local_elem(), libMesh::DofMap::n_local_dofs(), libMesh::MeshBase::n_local_elem(), libMesh::MeshBase::n_local_nodes(), and libMesh::MeshTools::weight().

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

libMesh::ParallelObject::_communicator

const Parallel::Communicator & _communicator

Definition: parallel_object.h:107

libMesh::Parallel::Communicator::rank

processor_id_type rank() const

Definition: communicator.h:173

◆ 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

virtualinherited

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 370 of file sparse_matrix.h.

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

◆ row_start()

template<typename T>

virtual numeric_index_type libMesh::PetscMatrix< T >::row_start ( ) const

overridevirtual

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

Implements libMesh::SparseMatrix< T >.

◆ row_stop()

template<typename T>

virtual numeric_index_type libMesh::PetscMatrix< T >::row_stop ( ) const

overridevirtual

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

Implements libMesh::SparseMatrix< T >.

◆ set()

template<typename T>

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

overridevirtual

Set the element (i,j) to value.

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

Implements libMesh::SparseMatrix< T >.

◆ set_destroy_mat_on_exit()

template<typename T>

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

virtual

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

◆ set_matrix_type()

template<typename T>

void libMesh::PetscMatrix< T >::set_matrix_type ( PetscMatrixType mat_type )

◆ swap()

template<typename T>

void libMesh::PetscMatrix< T >::swap ( PetscMatrix< T > & )

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

◆ update_preallocation_and_zero()

template<typename T>

void libMesh::PetscMatrix< T >::update_preallocation_and_zero ( )

Update the sparsity pattern based on dof_map, and set the matrix to zero.

This is useful in cases where the sparsity pattern changes during a computation.

◆ update_sparsity_pattern()

template<typename T>

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

virtualinherited

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 129 of file sparse_matrix.h.

129 {}

◆ 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.

◆ 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.

◆ zero()

template<typename T>

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

overridevirtual

Set all entries to 0.

Implements libMesh::SparseMatrix< T >.

◆ zero_rows()

template<typename T>

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

overridevirtual

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

Reimplemented from libMesh::SparseMatrix< T >.

Member Data Documentation

◆ _communicator

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

protectedinherited

Definition at line 107 of file parallel_object.h.

Referenced by libMesh::ParallelObject::comm(), libMesh::ParallelObject::n_processors(), libMesh::ParallelObject::operator=(), and libMesh::ParallelObject::processor_id().

◆ _counts

Counts libMesh::ReferenceCounter::_counts

staticprotectedinherited

Actually holds the data.

Definition at line 122 of file reference_counter.h.

Referenced by libMesh::ReferenceCounter::increment_constructor_count(), and libMesh::ReferenceCounter::increment_destructor_count().

◆ _destroy_mat_on_exit

template<typename T>

bool libMesh::PetscMatrix< T >::_destroy_mat_on_exit

private

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

Definition at line 283 of file petsc_matrix.h.

◆ _dof_map

template<typename T>

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

protectedinherited

The DofMap object associated with this object.

Definition at line 425 of file sparse_matrix.h.

Referenced by libMesh::SparseMatrix< Number >::attach_dof_map().

◆ _enable_print_counter

bool libMesh::ReferenceCounter::_enable_print_counter

staticprotectedinherited

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

Definition at line 141 of file reference_counter.h.

◆ _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 430 of file sparse_matrix.h.

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

◆ _mat

template<typename T>

Mat libMesh::PetscMatrix< T >::_mat

private

PETSc matrix datatype to store values.

Definition at line 277 of file petsc_matrix.h.

Referenced by libMesh::PetscMatrix< libMesh::Real >::mat().

◆ _mat_type

template<typename T>

PetscMatrixType libMesh::PetscMatrix< T >::_mat_type

private

Definition at line 285 of file petsc_matrix.h.

◆ _mutex

Threads::spin_mutex libMesh::ReferenceCounter::_mutex

staticprotectedinherited

Mutual exclusion object to enable thread-safe reference counting.

Definition at line 135 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 130 of file reference_counter.h.

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

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

include/numerics/petsc_matrix.h

Public Member Functions

Static Public Member Functions

Protected Types

Protected Member Functions

Protected Attributes

Static Protected Attributes

Private Attributes

Detailed Description

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

Member Typedef Documentation

◆ Counts

Constructor & Destructor Documentation

◆ PetscMatrix() [1/4]

◆ PetscMatrix() [2/4]

◆ PetscMatrix() [3/4]

◆ PetscMatrix() [4/4]

◆ ~PetscMatrix()

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]

◆ attach_dof_map()

◆ build()

◆ clear()

◆ close()

◆ closed()

◆ comm()

◆ create_submatrix()

◆ disable_print_counter_info()

◆ enable_print_counter_info()

◆ flush()

◆ get_diagonal()

◆ get_info()

◆ get_transpose()

◆ increment_constructor_count()

◆ increment_destructor_count()

◆ init() [1/3]

◆ init() [2/3]

◆ init() [3/3]

◆ initialized()

◆ l1_norm()

◆ linfty_norm()

◆ m()

◆ mat()

◆ n()

◆ n_objects()

◆ n_processors()

◆ need_full_sparsity_pattern()

◆ operator()()

◆ operator=() [1/2]

◆ operator=() [2/2]

◆ print()

◆ print_info()

◆ print_matlab()

◆ print_personal()

◆ processor_id()

◆ reinit_submatrix()

◆ row_start()

◆ row_stop()

◆ set()

◆ set_destroy_mat_on_exit()

◆ set_matrix_type()

◆ swap()

◆ update_preallocation_and_zero()

◆ update_sparsity_pattern()

◆ vector_mult()

◆ vector_mult_add()

◆ zero()

◆ zero_rows()

Member Data Documentation

◆ _communicator

◆ _counts

◆ _destroy_mat_on_exit

◆ _dof_map

◆ _enable_print_counter

◆ _is_initialized

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