#include <deal.II/lac/petsc_block_sparse_matrix.h>

Inheritance diagram for PETScWrappers::MPI::BlockSparseMatrix:

[legend]

Public Types
using	BaseClass = BlockMatrixBase<SparseMatrix>

using	BlockType = BaseClass::BlockType

using	value_type = BaseClass::value_type

using	pointer = BaseClass::pointer

using	const_pointer = BaseClass::const_pointer

using	reference = BaseClass::reference

using	const_reference = BaseClass::const_reference

using	size_type = BaseClass::size_type

using	iterator = BaseClass::iterator

using	const_iterator = BaseClass::const_iterator

using	real_type

Public Member Functions
	BlockSparseMatrix ()

	BlockSparseMatrix (const Mat &)

template<size_t block_rows, size_t block_columns>
	BlockSparseMatrix (const std::array< std::array< Mat, block_columns >, block_rows > &)

	~BlockSparseMatrix () override

BlockSparseMatrix &	operator= (const BlockSparseMatrix &)

BlockSparseMatrix &	operator= (const double d)

void	reinit (const size_type n_block_rows, const size_type n_block_columns)

void	reinit (const std::vector< IndexSet > &rows, const std::vector< IndexSet > &cols, const BlockDynamicSparsityPattern &bdsp, const MPI_Comm com)

void	reinit (const std::vector< IndexSet > &sizes, const BlockDynamicSparsityPattern &bdsp, const MPI_Comm com)

void	reinit (Mat A)

void	vmult (BlockVector &dst, const BlockVector &src) const

void	vmult (BlockVector &dst, const Vector &src) const

void	vmult (Vector &dst, const BlockVector &src) const

void	vmult (Vector &dst, const Vector &src) const

void	Tvmult (BlockVector &dst, const BlockVector &src) const

void	Tvmult (BlockVector &dst, const Vector &src) const

void	Tvmult (Vector &dst, const BlockVector &src) const

void	Tvmult (Vector &dst, const Vector &src) const

void	collect_sizes ()

void	compress (VectorOperation::values operation)

std::vector< IndexSet >	locally_owned_domain_indices () const

std::vector< IndexSet >	locally_owned_range_indices () const

std::uint64_t	n_nonzero_elements () const

MPI_Comm	get_mpi_communicator () const

	operator const Mat & () const

Mat &	petsc_matrix ()

BlockMatrixBase &	copy_from (const BlockMatrixType &source)

BlockType &	block (const unsigned int row, const unsigned int column)

const BlockType &	block (const unsigned int row, const unsigned int column) const

size_type	m () const

size_type	n () const

unsigned int	n_block_rows () const

unsigned int	n_block_cols () const

void	set (const size_type i, const size_type j, const value_type value)

void	set (const std::vector< size_type > &indices, const FullMatrix< number > &full_matrix, const bool elide_zero_values=false)

void	set (const std::vector< size_type > &row_indices, const std::vector< size_type > &col_indices, const FullMatrix< number > &full_matrix, const bool elide_zero_values=false)

void	set (const size_type row, const std::vector< size_type > &col_indices, const std::vector< number > &values, const bool elide_zero_values=false)

void	set (const size_type row, const size_type n_cols, const size_type col_indices, const number values, const bool elide_zero_values=false)

void	add (const size_type i, const size_type j, const value_type value)

void	add (const std::vector< size_type > &indices, const FullMatrix< number > &full_matrix, const bool elide_zero_values=true)

void	add (const std::vector< size_type > &row_indices, const std::vector< size_type > &col_indices, const FullMatrix< number > &full_matrix, const bool elide_zero_values=true)

void	add (const size_type row, const std::vector< size_type > &col_indices, const std::vector< number > &values, const bool elide_zero_values=true)

void	add (const size_type row, const size_type n_cols, const size_type col_indices, const number values, const bool elide_zero_values=true, const bool col_indices_are_sorted=false)

void	add (const value_type factor, const BlockMatrixBase< SparseMatrix > &matrix)

value_type	operator() (const size_type i, const size_type j) const

value_type	el (const size_type i, const size_type j) const

value_type	diag_element (const size_type i) const

BlockMatrixBase &	operator*= (const value_type factor)

BlockMatrixBase &	operator/= (const value_type factor)

void	vmult_add (BlockVectorType &dst, const BlockVectorType &src) const

void	Tvmult_add (BlockVectorType &dst, const BlockVectorType &src) const

value_type	matrix_norm_square (const BlockVectorType &v) const

real_type	frobenius_norm () const

value_type	matrix_scalar_product (const BlockVectorType &u, const BlockVectorType &v) const

value_type	residual (BlockVectorType &dst, const BlockVectorType &x, const BlockVectorType &b) const

void	print (std::ostream &out, const bool alternative_output=false) const

iterator	begin ()

iterator	begin (const size_type r)

const_iterator	begin () const

const_iterator	begin (const size_type r) const

iterator	end ()

iterator	end (const size_type r)

const_iterator	end () const

const_iterator	end (const size_type r) const

const BlockIndices &	get_row_indices () const

const BlockIndices &	get_column_indices () const

std::size_t	memory_consumption () const

template<class Archive >
void	serialize (Archive &ar, const unsigned int version)

Subscriptor functionality
Classes derived from Subscriptor provide a facility to subscribe to this object. This is mostly used by the SmartPointer class.
void	subscribe (std::atomic< bool > *const validity, const std::string &identifier="") const

void	unsubscribe (std::atomic< bool > *const validity, const std::string &identifier="") const

unsigned int	n_subscriptions () const

template<typename StreamType >
void	list_subscribers (StreamType &stream) const

void	list_subscribers () const

Static Public Member Functions
static ::ExceptionBase &	ExcIncompatibleRowNumbers (int arg1, int arg2, int arg3, int arg4)

static ::ExceptionBase &	ExcIncompatibleColNumbers (int arg1, int arg2, int arg3, int arg4)

static ::ExceptionBase &	ExcInUse (int arg1, std::string arg2, std::string arg3)

static ::ExceptionBase &	ExcNoSubscriber (std::string arg1, std::string arg2)

Protected Member Functions
void	clear ()

void	vmult_block_block (BlockVectorType &dst, const BlockVectorType &src) const

void	vmult_block_nonblock (BlockVectorType &dst, const VectorType &src) const

void	vmult_nonblock_block (VectorType &dst, const BlockVectorType &src) const

void	vmult_nonblock_nonblock (VectorType &dst, const VectorType &src) const

void	Tvmult_block_block (BlockVectorType &dst, const BlockVectorType &src) const

void	Tvmult_block_nonblock (BlockVectorType &dst, const VectorType &src) const

void	Tvmult_nonblock_block (VectorType &dst, const BlockVectorType &src) const

void	Tvmult_nonblock_nonblock (VectorType &dst, const VectorType &src) const

void	prepare_add_operation ()

void	prepare_set_operation ()

Protected Attributes
BlockIndices	row_block_indices

BlockIndices	column_block_indices

Table< 2, SmartPointer< BlockType, BlockMatrixBase< SparseMatrix > > >	sub_objects

Private Types
using	map_value_type = decltype(counter_map)::value_type

using	map_iterator = decltype(counter_map)::iterator

Private Member Functions
void	setup_nest_mat ()

void	create_empty_matrices_if_needed ()

void	check_no_subscribers () const noexcept

Private Attributes
Mat	petsc_nest_matrix

TemporaryData	temporary_data

std::atomic< unsigned int >	counter

std::map< std::string, unsigned int >	counter_map

std::vector< std::atomic< bool > * >	validity_pointers

const std::type_info *	object_info

Static Private Attributes
static std::mutex	mutex

Detailed Description

Blocked sparse matrix based on the PETScWrappers::MPI::SparseMatrix class. This class implements the functions that are specific to the PETSc SparseMatrix base objects for a blocked sparse matrix, and leaves the actual work relaying most of the calls to the individual blocks to the functions implemented in the base class. See there also for a description of when this class is useful.

In contrast to the deal.II-type SparseMatrix class, the PETSc matrices do not have external objects for the sparsity patterns. Thus, one does not determine the size of the individual blocks of a block matrix of this type by attaching a block sparsity pattern, but by calling reinit() to set the number of blocks and then by setting the size of each block separately. In order to fix the data structures of the block matrix, it is then necessary to let it know that we have changed the sizes of the underlying matrices. For this, one has to call the collect_sizes() function, for much the same reason as is documented with the BlockSparsityPattern class.

See also: Block (linear algebra)

Definition at line 66 of file petsc_block_sparse_matrix.h.

Member Typedef Documentation

◆ BaseClass

using PETScWrappers::MPI::BlockSparseMatrix::BaseClass = BlockMatrixBase<SparseMatrix>

Typedef the base class for simpler access to its own alias.

Definition at line 72 of file petsc_block_sparse_matrix.h.

◆ BlockType

using PETScWrappers::MPI::BlockSparseMatrix::BlockType = BaseClass::BlockType

Typedef the type of the underlying matrix.

Definition at line 77 of file petsc_block_sparse_matrix.h.

◆ value_type

using PETScWrappers::MPI::BlockSparseMatrix::value_type = BaseClass::value_type

Import the alias from the base class.

Definition at line 82 of file petsc_block_sparse_matrix.h.

◆ pointer

using PETScWrappers::MPI::BlockSparseMatrix::pointer = BaseClass::pointer

Definition at line 83 of file petsc_block_sparse_matrix.h.

◆ const_pointer

using PETScWrappers::MPI::BlockSparseMatrix::const_pointer = BaseClass::const_pointer

Definition at line 84 of file petsc_block_sparse_matrix.h.

◆ reference

using PETScWrappers::MPI::BlockSparseMatrix::reference = BaseClass::reference

Definition at line 85 of file petsc_block_sparse_matrix.h.

◆ const_reference

using PETScWrappers::MPI::BlockSparseMatrix::const_reference = BaseClass::const_reference

Definition at line 86 of file petsc_block_sparse_matrix.h.

◆ size_type

using PETScWrappers::MPI::BlockSparseMatrix::size_type = BaseClass::size_type

Definition at line 87 of file petsc_block_sparse_matrix.h.

◆ iterator

using PETScWrappers::MPI::BlockSparseMatrix::iterator = BaseClass::iterator

Definition at line 88 of file petsc_block_sparse_matrix.h.

◆ const_iterator

using PETScWrappers::MPI::BlockSparseMatrix::const_iterator = BaseClass::const_iterator

Definition at line 89 of file petsc_block_sparse_matrix.h.

◆ real_type

using BlockMatrixBase< SparseMatrix >::real_type

inherited

Definition at line 362 of file block_matrix_base.h.

◆ map_value_type

using Subscriptor::map_value_type = decltype(counter_map)::value_type

privateinherited

The data type used in counter_map.

Definition at line 229 of file subscriptor.h.

◆ map_iterator

using Subscriptor::map_iterator = decltype(counter_map)::iterator

privateinherited

The iterator type used in counter_map.

Definition at line 234 of file subscriptor.h.

Constructor & Destructor Documentation

◆ BlockSparseMatrix() [1/3]

BlockSparseMatrix< number >::BlockSparseMatrix ( )

inline

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 reinit(BlockSparsityPattern). The number of blocks per row and column are then determined by that function.

Definition at line 358 of file petsc_block_sparse_matrix.h.

◆ BlockSparseMatrix() [2/3]

BlockSparseMatrix< number >::BlockSparseMatrix ( const Mat & A )

inlineexplicit

Create a BlockSparseMatrix with a PETSc Mat that describes the entire block matrix. It infers the number of blocks from the Mat if it is of type MATNEST, otherwise the block operator will only have a single block. Internally, we always store a MATNEST matrix.

Definition at line 365 of file petsc_block_sparse_matrix.h.

◆ BlockSparseMatrix() [3/3]

template<size_t block_rows, size_t block_columns>

BlockSparseMatrix< block_rows, block_columns >::BlockSparseMatrix ( const std::array< std::array< Mat, block_columns >, block_rows > & arrayA )

inlineexplicit

Create a BlockSparseMatrix with an array of PETSc matrices.

Definition at line 374 of file petsc_block_sparse_matrix.h.

◆ ~BlockSparseMatrix()

BlockSparseMatrix< number >::~BlockSparseMatrix ( )

override

Destructor.

Definition at line 72 of file petsc_parallel_block_sparse_matrix.cc.

Member Function Documentation

◆ operator=() [1/2]

BlockSparseMatrix & BlockSparseMatrix< number >::operator= ( const BlockSparseMatrix & m )

Pseudo copy operator only copying empty objects. The sizes of the block matrices need to be the same.

Definition at line 63 of file petsc_parallel_block_sparse_matrix.cc.

◆ operator=() [2/2]

BlockSparseMatrix & BlockSparseMatrix< number >::operator= ( const double d )

inline

This operator assigns a scalar to a matrix. Since this does usually not make much sense (should we set all matrix entries to this value? Only the nonzero entries of the sparsity pattern?), this operation is only allowed if the actual value to be assigned is zero. This operator only exists to allow for the obvious notation matrix=0, which sets all elements of the matrix to zero, but keep the sparsity pattern previously used.

Definition at line 394 of file petsc_block_sparse_matrix.h.

◆ reinit() [1/4]

void PETScWrappers::MPI::BlockSparseMatrix::reinit	(	const size_type	n_block_rows,
		const size_type	n_block_columns )

Resize the matrix, by setting the number of block rows and columns. This deletes all blocks and replaces them with uninitialized ones, i.e. ones for which also the sizes are not yet set. You have to do that by calling the reinit functions of the blocks themselves. Do not forget to call collect_sizes() after that on this object.

The reason that you have to set sizes of the blocks yourself is that the sizes may be varying, the maximum number of elements per row may be varying, etc. It is simpler not to reproduce the interface of the SparsityPattern class here but rather let the user call whatever function they desire.

◆ reinit() [2/4]

void BlockSparseMatrix< number >::reinit	(	const std::vector< IndexSet > &	rows,
		const std::vector< IndexSet > &	cols,
		const BlockDynamicSparsityPattern &	bdsp,
		const MPI_Comm	com )

Efficiently reinit the block matrix for a parallel computation. Only the BlockSparsityPattern of the Simple type can efficiently store large sparsity patterns in parallel, so this is the only supported argument. The IndexSets describe the locally owned range of DoFs for each block. Note that the IndexSets needs to be ascending and 1:1. For a symmetric structure hand in the same vector for the first two arguments.

Definition at line 110 of file petsc_parallel_block_sparse_matrix.cc.

◆ reinit() [3/4]

void BlockSparseMatrix< number >::reinit	(	const std::vector< IndexSet > &	sizes,
		const BlockDynamicSparsityPattern &	bdsp,
		const MPI_Comm	com )

Same as above but for a symmetric structure only.

Definition at line 149 of file petsc_parallel_block_sparse_matrix.cc.

◆ reinit() [4/4]

void BlockSparseMatrix< number >::reinit ( Mat A )

This method associates the PETSc Mat to the instance of the class. Infers the number of blocks from A if it is of type MATNEST, otherwise the block operator will only have a single block.

Definition at line 334 of file petsc_parallel_block_sparse_matrix.cc.

◆ vmult() [1/4]

void BlockSparseMatrix< number >::vmult	(	BlockVector &	dst,
		const BlockVector &	src ) const

inline

Matrix-vector multiplication: let \(dst = M*src\) with \(M\) being this matrix.

Definition at line 408 of file petsc_block_sparse_matrix.h.

◆ vmult() [2/4]

void BlockSparseMatrix< number >::vmult	(	BlockVector &	dst,
		const Vector &	src ) const

inline

Matrix-vector multiplication. Just like the previous function, but only applicable if the matrix has only one block column.

Definition at line 416 of file petsc_block_sparse_matrix.h.

◆ vmult() [3/4]

void BlockSparseMatrix< number >::vmult	(	Vector &	dst,
		const BlockVector &	src ) const

inline

Matrix-vector multiplication. Just like the previous function, but only applicable if the matrix has only one block row.

Definition at line 424 of file petsc_block_sparse_matrix.h.

◆ vmult() [4/4]

void BlockSparseMatrix< number >::vmult	(	Vector &	dst,
		const Vector &	src ) const

inline

Matrix-vector multiplication. Just like the previous function, but only applicable if the matrix has only one block.

Definition at line 432 of file petsc_block_sparse_matrix.h.

◆ Tvmult() [1/4]

void BlockSparseMatrix< number >::Tvmult	(	BlockVector &	dst,
		const BlockVector &	src ) const

inline

Matrix-vector multiplication: let \(dst = M^T*src\) with \(M\) being this matrix. This function does the same as vmult() but takes the transposed matrix.

Definition at line 439 of file petsc_block_sparse_matrix.h.

◆ Tvmult() [2/4]

void BlockSparseMatrix< number >::Tvmult	(	BlockVector &	dst,
		const Vector &	src ) const

inline

Matrix-vector multiplication. Just like the previous function, but only applicable if the matrix has only one block row.

Definition at line 447 of file petsc_block_sparse_matrix.h.

◆ Tvmult() [3/4]

void BlockSparseMatrix< number >::Tvmult	(	Vector &	dst,
		const BlockVector &	src ) const

inline

Matrix-vector multiplication. Just like the previous function, but only applicable if the matrix has only one block column.

Definition at line 455 of file petsc_block_sparse_matrix.h.

◆ Tvmult() [4/4]

void BlockSparseMatrix< number >::Tvmult	(	Vector &	dst,
		const Vector &	src ) const

inline

Matrix-vector multiplication. Just like the previous function, but only applicable if the matrix has only one block.

Definition at line 463 of file petsc_block_sparse_matrix.h.

◆ collect_sizes()

void BlockSparseMatrix< number >::collect_sizes ( )

This function collects the sizes of the sub-objects and stores them in internal arrays, in order to be able to relay global indices into the matrix to indices into the subobjects. You must call this function each time after you have changed the size of the sub-objects.

Definition at line 231 of file petsc_parallel_block_sparse_matrix.cc.

◆ compress()

void BlockSparseMatrix< number >::compress ( VectorOperation::values operation )

Call the compress() function on all the subblocks of the matrix and update the internal state of the PETSc object.

See Compressing distributed objects for more information.

Definition at line 267 of file petsc_parallel_block_sparse_matrix.cc.

◆ locally_owned_domain_indices()

std::vector< IndexSet > BlockSparseMatrix< number >::locally_owned_domain_indices ( ) const

Return the partitioning of the domain space of this matrix, i.e., the partitioning of the vectors this matrix has to be multiplied with.

Definition at line 276 of file petsc_parallel_block_sparse_matrix.cc.

◆ locally_owned_range_indices()

std::vector< IndexSet > BlockSparseMatrix< number >::locally_owned_range_indices ( ) const

Return the partitioning of the range space of this matrix, i.e., the partitioning of the vectors that are result from matrix-vector products.

Definition at line 289 of file petsc_parallel_block_sparse_matrix.cc.

◆ n_nonzero_elements()

std::uint64_t BlockSparseMatrix< number >::n_nonzero_elements ( ) const

Return the number of nonzero elements of this matrix. Actually, it returns the number of entries in the sparsity pattern; if any of the entries should happen to be zero, it is counted anyway.

Definition at line 302 of file petsc_parallel_block_sparse_matrix.cc.

◆ get_mpi_communicator()

MPI_Comm BlockSparseMatrix< number >::get_mpi_communicator ( ) const

Return the underlying MPI communicator.

Definition at line 315 of file petsc_parallel_block_sparse_matrix.cc.

◆ operator const Mat &()

BlockSparseMatrix< number >::operator const Mat & ( ) const

Conversion operator to gain access to the underlying PETSc type. If you do this, you cut this class off some information it may need, so this conversion operator should only be used if you know what you do. In particular, it should only be used for read-only operations into the matrix.

Definition at line 320 of file petsc_parallel_block_sparse_matrix.cc.

◆ petsc_matrix()

Mat & BlockSparseMatrix< number >::petsc_matrix ( )

Return a reference to the underlying PETSc type. It can be used to modify the underlying data, so use it only when you know what you are doing.

The PETSc Mat object returned here describes the entire matrix, not just one of its blocks. Internally, this is done using a "nested" matrix using PETSc's MATNEST object whose individual blocks are the blocks of this matrix.

Definition at line 328 of file petsc_parallel_block_sparse_matrix.cc.

◆ setup_nest_mat()

void BlockSparseMatrix< number >::setup_nest_mat ( )

private

Utility to set up the MATNEST object.

Definition at line 239 of file petsc_parallel_block_sparse_matrix.cc.

◆ create_empty_matrices_if_needed()

void BlockSparseMatrix< number >::create_empty_matrices_if_needed ( )

private

An utility method to populate empty blocks with actual objects. This is needed because MATNEST supports nullptr as a block, while the BlockMatrixBase class does not.

Definition at line 159 of file petsc_parallel_block_sparse_matrix.cc.

◆ copy_from()

BlockMatrixBase & BlockMatrixBase< SparseMatrix >::copy_from ( const BlockMatrixType & source )

inherited

Copy the matrix given as argument into the current object.

Copying matrices is an expensive operation that we do not want to happen by accident through compiler generated code for operator=. (This would happen, for example, if one accidentally declared a function argument of the current type by value rather than by reference.) The functionality of copying matrices is implemented in this member function instead. All copy operations of objects of this type therefore require an explicit function call.

The source matrix may be a matrix of arbitrary type, as long as its data type is convertible to the data type of this matrix.

The function returns a reference to this.

◆ block() [1/2]

BlockType & BlockMatrixBase< SparseMatrix >::block	(	const unsigned int	row,
		const unsigned int	column )

inherited

Access the block with the given coordinates.

◆ block() [2/2]

const BlockType & BlockMatrixBase< SparseMatrix >::block	(	const unsigned int	row,
		const unsigned int	column ) const

inherited

Access the block with the given coordinates. Version for constant objects.

◆ m()

size_type BlockMatrixBase< SparseMatrix >::m ( ) const

inherited

Return the dimension of the codomain (or range) space. Note that the matrix is of dimension \(m \times n\).

◆ n()

size_type BlockMatrixBase< SparseMatrix >::n ( ) const

inherited

Return the dimension of the domain space. Note that the matrix is of dimension \(m \times n\).

◆ n_block_rows()

unsigned int BlockMatrixBase< SparseMatrix >::n_block_rows ( ) const

inherited

Return the number of blocks in a column. Returns zero if no sparsity pattern is presently associated to this matrix.

◆ n_block_cols()

unsigned int BlockMatrixBase< SparseMatrix >::n_block_cols ( ) const

inherited

Return the number of blocks in a row. Returns zero if no sparsity pattern is presently associated to this matrix.

◆ set() [1/5]

void BlockMatrixBase< SparseMatrix >::set	(	const size_type	i,
		const size_type	j,
		const value_type	value )

inherited

Set the element (i,j) to value. Throws an error if the entry does not exist or if value is not a finite number. Still, it is allowed to store zero values in non-existent fields.

◆ set() [2/5]

void BlockMatrixBase< SparseMatrix >::set	(	const std::vector< size_type > &	indices,
		const FullMatrix< number > &	full_matrix,
		const bool	elide_zero_values = false )

inherited

Set all elements given in a FullMatrix into the sparse matrix locations given by indices. In other words, this function writes the elements in full_matrix into the calling matrix, using the local-to-global indexing specified by indices for both the rows and the columns of the matrix. This function assumes a quadratic sparse matrix and a quadratic full_matrix, the usual situation in FE calculations.

The optional parameter elide_zero_values can be used to specify whether zero values should be set anyway or they should be filtered away (and not change the previous content in the respective element if it exists). The default value is false, i.e., even zero values are treated.

◆ set() [3/5]

void BlockMatrixBase< SparseMatrix >::set	(	const std::vector< size_type > &	row_indices,
		const std::vector< size_type > &	col_indices,
		const FullMatrix< number > &	full_matrix,
		const bool	elide_zero_values = false )

inherited

Same function as before, but now including the possibility to use rectangular full_matrices and different local-to-global indexing on rows and columns, respectively.

◆ set() [4/5]

void BlockMatrixBase< SparseMatrix >::set	(	const size_type	row,
		const std::vector< size_type > &	col_indices,
		const std::vector< number > &	values,
		const bool	elide_zero_values = false )

inherited

Set several elements in the specified row of the matrix with column indices as given by col_indices to the respective value.

The optional parameter elide_zero_values can be used to specify whether zero values should be set anyway or they should be filtered away (and not change the previous content in the respective element if it exists). The default value is false, i.e., even zero values are treated.

◆ set() [5/5]

void BlockMatrixBase< SparseMatrix >::set	(	const size_type	row,
		const size_type	n_cols,
		const size_type *	col_indices,
		const number *	values,
		const bool	elide_zero_values = false )

inherited

Set several elements to values given by values in a given row in columns given by col_indices into the sparse matrix.

The optional parameter elide_zero_values can be used to specify whether zero values should be inserted anyway or they should be filtered away. The default value is false, i.e., even zero values are inserted/replaced.

◆ add() [1/6]

void BlockMatrixBase< SparseMatrix >::add	(	const size_type	i,
		const size_type	j,
		const value_type	value )

inherited

Add value to the element (i,j). Throws an error if the entry does not exist or if value is not a finite number. Still, it is allowed to store zero values in non-existent fields.

◆ add() [2/6]

void BlockMatrixBase< SparseMatrix >::add	(	const std::vector< size_type > &	indices,
		const FullMatrix< number > &	full_matrix,
		const bool	elide_zero_values = true )

inherited

Add all elements given in a FullMatrix<double> into sparse matrix locations given by indices. In other words, this function adds the elements in full_matrix to the respective entries in calling matrix, using the local-to-global indexing specified by indices for both the rows and the columns of the matrix. This function assumes a quadratic sparse matrix and a quadratic full_matrix, the usual situation in FE calculations.

The optional parameter elide_zero_values can be used to specify whether zero values should be added anyway or these should be filtered away and only non-zero data is added. The default value is true, i.e., zero values won't be added into the matrix.

◆ add() [3/6]

void BlockMatrixBase< SparseMatrix >::add	(	const std::vector< size_type > &	row_indices,
		const std::vector< size_type > &	col_indices,
		const FullMatrix< number > &	full_matrix,
		const bool	elide_zero_values = true )

inherited

Same function as before, but now including the possibility to use rectangular full_matrices and different local-to-global indexing on rows and columns, respectively.

◆ add() [4/6]

void BlockMatrixBase< SparseMatrix >::add	(	const size_type	row,
		const std::vector< size_type > &	col_indices,
		const std::vector< number > &	values,
		const bool	elide_zero_values = true )

inherited

Set several elements in the specified row of the matrix with column indices as given by col_indices to the respective value.

The optional parameter elide_zero_values can be used to specify whether zero values should be added anyway or these should be filtered away and only non-zero data is added. The default value is true, i.e., zero values won't be added into the matrix.

◆ add() [5/6]

void BlockMatrixBase< SparseMatrix >::add	(	const size_type	row,
		const size_type	n_cols,
		const size_type *	col_indices,
		const number *	values,
		const bool	elide_zero_values = true,
		const bool	col_indices_are_sorted = false )

inherited

Add an array of values given by values in the given global matrix row at columns specified by col_indices in the sparse matrix.

The optional parameter elide_zero_values can be used to specify whether zero values should be added anyway or these should be filtered away and only non-zero data is added. The default value is true, i.e., zero values won't be added into the matrix.

◆ add() [6/6]

void BlockMatrixBase< SparseMatrix >::add	(	const value_type	factor,
		const BlockMatrixBase< SparseMatrix > &	matrix )

inherited

Add matrix scaled by factor to this matrix, i.e. the matrix factor*matrix is added to this. If the sparsity pattern of the calling matrix does not contain all the elements in the sparsity pattern of the input matrix, this function will throw an exception.

Depending on MatrixType, however, additional restrictions might arise. Some sparse matrix formats require matrix to be based on the same sparsity pattern as the calling matrix.

◆ operator()()

value_type BlockMatrixBase< SparseMatrix >::operator()	(	const size_type	i,
		const size_type	j ) const

inherited

Return the value of the entry (i,j). This may be an expensive operation and you should always take care where to call this function. In order to avoid abuse, this function throws an exception if the wanted element does not exist in the matrix.

◆ el()

value_type BlockMatrixBase< SparseMatrix >::el	(	const size_type	i,
		const size_type	j ) const

inherited

This function is mostly like operator()() in that it returns the value of the matrix entry (i,j). The only difference is that if this entry does not exist in the sparsity pattern, then instead of raising an exception, zero is returned. While this may be convenient in some cases, note that it is simple to write algorithms that are slow compared to an optimal solution, since the sparsity of the matrix is not used.

◆ diag_element()

value_type BlockMatrixBase< SparseMatrix >::diag_element ( const size_type i ) const

inherited

Return the main diagonal element in the ith row. This function throws an error if the matrix is not quadratic and also if the diagonal blocks of the matrix are not quadratic.

This function is considerably faster than the operator()(), since for quadratic matrices, the diagonal entry may be the first to be stored in each row and access therefore does not involve searching for the right column number.

◆ operator*=()

BlockMatrixBase & BlockMatrixBase< SparseMatrix >::operator*= ( const value_type factor )

inherited

Multiply the entire matrix by a fixed factor.

◆ operator/=()

BlockMatrixBase & BlockMatrixBase< SparseMatrix >::operator/= ( const value_type factor )

inherited

Divide the entire matrix by a fixed factor.

◆ vmult_add()

void BlockMatrixBase< SparseMatrix >::vmult_add	(	BlockVectorType &	dst,
		const BlockVectorType &	src ) const

inherited

Adding Matrix-vector multiplication. Add \(M*src\) on \(dst\) with \(M\) being this matrix.

◆ Tvmult_add()

void BlockMatrixBase< SparseMatrix >::Tvmult_add	(	BlockVectorType &	dst,
		const BlockVectorType &	src ) const

inherited

Adding Matrix-vector multiplication. Add M^Tsrc to dst with M being this matrix. This function does the same as vmult_add() but takes the transposed matrix.

◆ matrix_norm_square()

value_type BlockMatrixBase< SparseMatrix >::matrix_norm_square ( const BlockVectorType & v ) const

inherited

Return the norm of the vector v with respect to the norm induced by this matrix, i.e. v^TMv). This is useful, e.g. in the finite element context, where the L^T-norm of a function equals the matrix norm with respect to the mass matrix of the vector representing the nodal values of the finite element function. Note that even though the function's name might suggest something different, for historic reasons not the norm but its square is returned, as defined above by the scalar product.

Obviously, the matrix needs to be square for this operation.

◆ frobenius_norm()

real_type BlockMatrixBase< SparseMatrix >::frobenius_norm ( ) const

inherited

Return the frobenius norm of the matrix, i.e. the square root of the sum of squares of all entries in the matrix.

◆ matrix_scalar_product()

value_type BlockMatrixBase< SparseMatrix >::matrix_scalar_product	(	const BlockVectorType &	u,
		const BlockVectorType &	v ) const

inherited

Compute the matrix scalar product \(\left(u,Mv\right)\).

◆ residual()

value_type BlockMatrixBase< SparseMatrix >::residual	(	BlockVectorType &	dst,
		const BlockVectorType &	x,
		const BlockVectorType &	b ) const

inherited

Compute the residual r=b-Ax. Write the residual into dst.

◆ print()

void BlockMatrixBase< SparseMatrix >::print	(	std::ostream &	out,
		const bool	alternative_output = false ) const

inherited

Print the matrix to the given stream, using the format (line,col) value, i.e. one nonzero entry of the matrix per line. The optional flag outputs the sparsity pattern in a different style according to the underlying sparse matrix type.

◆ begin() [1/4]

iterator BlockMatrixBase< SparseMatrix >::begin ( )

inherited

Iterator starting at the first entry.

◆ begin() [2/4]

iterator BlockMatrixBase< SparseMatrix >::begin ( const size_type r )

inherited

Iterator starting at the first entry of row r.

◆ begin() [3/4]

const_iterator BlockMatrixBase< SparseMatrix >::begin ( ) const

inherited

Iterator starting at the first entry.

◆ begin() [4/4]

const_iterator BlockMatrixBase< SparseMatrix >::begin ( const size_type r ) const

inherited

Iterator starting at the first entry of row r.

◆ end() [1/4]

iterator BlockMatrixBase< SparseMatrix >::end ( )

inherited

Final iterator.

◆ end() [2/4]

iterator BlockMatrixBase< SparseMatrix >::end ( const size_type r )

inherited

Final iterator of row r.

◆ end() [3/4]

const_iterator BlockMatrixBase< SparseMatrix >::end ( ) const

inherited

Final iterator.

◆ end() [4/4]

const_iterator BlockMatrixBase< SparseMatrix >::end ( const size_type r ) const

inherited

Final iterator of row r.

◆ get_row_indices()

const BlockIndices & BlockMatrixBase< SparseMatrix >::get_row_indices ( ) const

inherited

Return a reference to the underlying BlockIndices data of the rows.

◆ get_column_indices()

const BlockIndices & BlockMatrixBase< SparseMatrix >::get_column_indices ( ) const

inherited

Return a reference to the underlying BlockIndices data of the columns.

◆ memory_consumption()

std::size_t BlockMatrixBase< SparseMatrix >::memory_consumption ( ) const

inherited

Determine an estimate for the memory consumption (in bytes) of this object. Note that only the memory reserved on the current processor is returned in case this is called in an MPI-based program.

◆ ExcIncompatibleRowNumbers()

static ::ExceptionBase & BlockMatrixBase< SparseMatrix >::ExcIncompatibleRowNumbers	(	int	arg1,
		int	arg2,
		int	arg3,
		int	arg4 )

staticinherited

Exception

Note: The message that will be printed by this exception reads:
<< "The blocks [" << arg1 << ',' << arg2 << "] and [" << arg3 << ',' << arg4 << "] have differing row numbers."

◆ ExcIncompatibleColNumbers()

static ::ExceptionBase & BlockMatrixBase< SparseMatrix >::ExcIncompatibleColNumbers	(	int	arg1,
		int	arg2,
		int	arg3,
		int	arg4 )

staticinherited

Exception

Note: The message that will be printed by this exception reads:
<< "The blocks [" << arg1 << ',' << arg2 << "] and [" << arg3 << ',' << arg4 << "] have differing column numbers."

◆ clear()

void BlockMatrixBase< SparseMatrix >::clear ( )

protectedinherited

Release all memory and return to a state just like after having called the default constructor. It also forgets the sparsity pattern it was previously tied to.

This calls clear for all sub-matrices and then resets this object to have no blocks at all.

This function is protected since it may be necessary to release additional structures. A derived class can make it public again, if it is sufficient.

◆ vmult_block_block()

void BlockMatrixBase< SparseMatrix >::vmult_block_block	(	BlockVectorType &	dst,
		const BlockVectorType &	src ) const

protectedinherited

Matrix-vector multiplication: let \(dst = M*src\) with \(M\) being this matrix.

Due to problems with deriving template arguments between the block and non-block versions of the vmult/Tvmult functions, the actual functions are implemented in derived classes, with implementations forwarding the calls to the implementations provided here under a unique name for which template arguments can be derived by the compiler.

◆ vmult_block_nonblock()

void BlockMatrixBase< SparseMatrix >::vmult_block_nonblock	(	BlockVectorType &	dst,
		const VectorType &	src ) const

protectedinherited

Matrix-vector multiplication. Just like the previous function, but only applicable if the matrix has only one block column.

Due to problems with deriving template arguments between the block and non-block versions of the vmult/Tvmult functions, the actual functions are implemented in derived classes, with implementations forwarding the calls to the implementations provided here under a unique name for which template arguments can be derived by the compiler.

◆ vmult_nonblock_block()

void BlockMatrixBase< SparseMatrix >::vmult_nonblock_block	(	VectorType &	dst,
		const BlockVectorType &	src ) const

protectedinherited

Matrix-vector multiplication. Just like the previous function, but only applicable if the matrix has only one block row.

Due to problems with deriving template arguments between the block and non-block versions of the vmult/Tvmult functions, the actual functions are implemented in derived classes, with implementations forwarding the calls to the implementations provided here under a unique name for which template arguments can be derived by the compiler.

◆ vmult_nonblock_nonblock()

void BlockMatrixBase< SparseMatrix >::vmult_nonblock_nonblock	(	VectorType &	dst,
		const VectorType &	src ) const

protectedinherited

Matrix-vector multiplication. Just like the previous function, but only applicable if the matrix has only one block.

Due to problems with deriving template arguments between the block and non-block versions of the vmult/Tvmult functions, the actual functions are implemented in derived classes, with implementations forwarding the calls to the implementations provided here under a unique name for which template arguments can be derived by the compiler.

◆ Tvmult_block_block()

void BlockMatrixBase< SparseMatrix >::Tvmult_block_block	(	BlockVectorType &	dst,
		const BlockVectorType &	src ) const

protectedinherited

Matrix-vector multiplication: let \(dst = M^T*src\) with \(M\) being this matrix. This function does the same as vmult() but takes the transposed matrix.

Due to problems with deriving template arguments between the block and non-block versions of the vmult/Tvmult functions, the actual functions are implemented in derived classes, with implementations forwarding the calls to the implementations provided here under a unique name for which template arguments can be derived by the compiler.

◆ Tvmult_block_nonblock()

void BlockMatrixBase< SparseMatrix >::Tvmult_block_nonblock	(	BlockVectorType &	dst,
		const VectorType &	src ) const

protectedinherited

Matrix-vector multiplication. Just like the previous function, but only applicable if the matrix has only one block row.

Due to problems with deriving template arguments between the block and non-block versions of the vmult/Tvmult functions, the actual functions are implemented in derived classes, with implementations forwarding the calls to the implementations provided here under a unique name for which template arguments can be derived by the compiler.

◆ Tvmult_nonblock_block()

void BlockMatrixBase< SparseMatrix >::Tvmult_nonblock_block	(	VectorType &	dst,
		const BlockVectorType &	src ) const

protectedinherited

Matrix-vector multiplication. Just like the previous function, but only applicable if the matrix has only one block column.

Due to problems with deriving template arguments between the block and non-block versions of the vmult/Tvmult functions, the actual functions are implemented in derived classes, with implementations forwarding the calls to the implementations provided here under a unique name for which template arguments can be derived by the compiler.

◆ Tvmult_nonblock_nonblock()

void BlockMatrixBase< SparseMatrix >::Tvmult_nonblock_nonblock	(	VectorType &	dst,
		const VectorType &	src ) const

protectedinherited

Matrix-vector multiplication. Just like the previous function, but only applicable if the matrix has only one block.

Due to problems with deriving template arguments between the block and non-block versions of the vmult/Tvmult functions, the actual functions are implemented in derived classes, with implementations forwarding the calls to the implementations provided here under a unique name for which template arguments can be derived by the compiler.

◆ prepare_add_operation()

void BlockMatrixBase< SparseMatrix >::prepare_add_operation ( )

protectedinherited

Some matrix types, in particular PETSc, need to synchronize set and add operations. This has to be done for all matrices in the BlockMatrix. This routine prepares adding of elements by notifying all blocks. Called by all internal routines before adding elements.

◆ prepare_set_operation()

void BlockMatrixBase< SparseMatrix >::prepare_set_operation ( )

protectedinherited

Notifies all blocks to let them prepare for setting elements, see prepare_add_operation().

◆ subscribe()

void Subscriptor::subscribe	(	std::atomic< bool > *const	validity,
		const std::string &	identifier = "" ) const

inherited

Subscribes a user of the object by storing the pointer validity. The subscriber may be identified by text supplied as identifier.

Definition at line 135 of file subscriptor.cc.

◆ unsubscribe()

void Subscriptor::unsubscribe	(	std::atomic< bool > *const	validity,
		const std::string &	identifier = "" ) const

inherited

Unsubscribes a user from the object.

Note: The identifier and the validity pointer must be the same as the one supplied to subscribe().

Definition at line 155 of file subscriptor.cc.

◆ n_subscriptions()

unsigned int Subscriptor::n_subscriptions ( ) const

inlineinherited

Return the present number of subscriptions to this object. This allows to use this class for reference counted lifetime determination where the last one to unsubscribe also deletes the object.

Definition at line 300 of file subscriptor.h.

◆ list_subscribers() [1/2]

template<typename StreamType >

void Subscriptor::list_subscribers ( StreamType & stream ) const

inlineinherited

List the subscribers to the input stream.

Definition at line 317 of file subscriptor.h.

◆ list_subscribers() [2/2]

void Subscriptor::list_subscribers ( ) const

inherited

List the subscribers to deallog.

Definition at line 203 of file subscriptor.cc.

◆ serialize()

template<class Archive >

void Subscriptor::serialize	(	Archive &	ar,
		const unsigned int	version )

inlineinherited

Read or write the data of this object to or from a stream for the purpose of serialization using the BOOST serialization library.

This function does not actually serialize any of the member variables of this class. The reason is that what this class stores is only who subscribes to this object, but who does so at the time of storing the contents of this object does not necessarily have anything to do with who subscribes to the object when it is restored. Consequently, we do not want to overwrite the subscribers at the time of restoring, and then there is no reason to write the subscribers out in the first place.

Definition at line 309 of file subscriptor.h.

◆ check_no_subscribers()

void Subscriptor::check_no_subscribers ( ) const

privatenoexceptinherited

Check that there are no objects subscribing to this object. If this check passes then it is safe to destroy the current object. It this check fails then this function will either abort or print an error message to deallog (by using the AssertNothrow mechanism), but will not throw an exception.

Note: Since this function is just a consistency check it does nothing in release mode.; If this function is called when there is an uncaught exception then, rather than aborting, this function prints an error message to the standard error stream and returns.

Definition at line 52 of file subscriptor.cc.

Member Data Documentation

◆ petsc_nest_matrix

Mat PETScWrappers::MPI::BlockSparseMatrix::petsc_nest_matrix

private

A PETSc Mat object that describes the entire block matrix. Internally, this is done by creating a "nested" matrix using PETSc's MATNEST object whose individual blocks are the blocks of this matrix.

Definition at line 336 of file petsc_block_sparse_matrix.h.

◆ row_block_indices

BlockIndices BlockMatrixBase< SparseMatrix >::row_block_indices

protectedinherited

Index arrays for rows and columns.

Definition at line 846 of file block_matrix_base.h.

◆ column_block_indices

BlockIndices BlockMatrixBase< SparseMatrix >::column_block_indices

protectedinherited

Definition at line 847 of file block_matrix_base.h.

◆ sub_objects

Table<2, SmartPointer<BlockType, BlockMatrixBase<SparseMatrix> > > BlockMatrixBase< SparseMatrix >::sub_objects

protectedinherited

Array of sub-matrices.

Definition at line 852 of file block_matrix_base.h.

◆ temporary_data

TemporaryData BlockMatrixBase< SparseMatrix >::temporary_data

privateinherited

A set of scratch arrays that can be used by the add() and set() functions that take pointers to data to pre-sort indices before use. Access from multiple threads is synchronized via the mutex variable that is part of the structure.

Definition at line 1064 of file block_matrix_base.h.

◆ counter

std::atomic<unsigned int> Subscriptor::counter

mutableprivateinherited

Store the number of objects which subscribed to this object. Initially, this number is zero, and upon destruction it shall be zero again (i.e. all objects which subscribed should have unsubscribed again).

The creator (and owner) of an object is counted in the map below if HE manages to supply identification.

We use the mutable keyword in order to allow subscription to constant objects also.

This counter may be read from and written to concurrently in multithreaded code: hence we use the std::atomic class template.

Definition at line 218 of file subscriptor.h.

◆ counter_map

std::map<std::string, unsigned int> Subscriptor::counter_map

mutableprivateinherited

In this map, we count subscriptions for each different identification string supplied to subscribe().

Definition at line 224 of file subscriptor.h.

◆ validity_pointers

std::vector<std::atomic<bool> *> Subscriptor::validity_pointers

mutableprivateinherited

In this vector, we store pointers to the validity bool in the SmartPointer objects that subscribe to this class.

Definition at line 240 of file subscriptor.h.

◆ object_info

const std::type_info* Subscriptor::object_info

mutableprivateinherited

Pointer to the typeinfo object of this object, from which we can later deduce the class name. Since this information on the derived class is neither available in the destructor, nor in the constructor, we obtain it in between and store it here.

Definition at line 248 of file subscriptor.h.

◆ mutex

std::mutex Subscriptor::mutex

staticprivateinherited

A mutex used to ensure data consistency when accessing the mutable members of this class. This lock is used in the subscribe() and unsubscribe() functions, as well as in list_subscribers().

Definition at line 271 of file subscriptor.h.

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

include/deal.II/lac/petsc_block_sparse_matrix.h
source/lac/petsc_parallel_block_sparse_matrix.cc

Public Types

Public Member Functions

Static Public Member Functions

Protected Member Functions

Protected Attributes

Private Types

Private Member Functions

Private Attributes

Static Private Attributes

Detailed Description

Member Typedef Documentation

◆ BaseClass

◆ BlockType

◆ value_type

◆ pointer

◆ const_pointer

◆ reference

◆ const_reference

◆ size_type

◆ iterator

◆ const_iterator

◆ real_type

◆ map_value_type

◆ map_iterator

Constructor & Destructor Documentation

◆ BlockSparseMatrix() [1/3]

◆ BlockSparseMatrix() [2/3]

◆ BlockSparseMatrix() [3/3]

◆ ~BlockSparseMatrix()

Member Function Documentation

◆ operator=() [1/2]

◆ operator=() [2/2]

◆ reinit() [1/4]

◆ reinit() [2/4]

◆ reinit() [3/4]

◆ reinit() [4/4]

◆ vmult() [1/4]

◆ vmult() [2/4]

◆ vmult() [3/4]

◆ vmult() [4/4]

◆ Tvmult() [1/4]

◆ Tvmult() [2/4]

◆ Tvmult() [3/4]

◆ Tvmult() [4/4]

◆ collect_sizes()

◆ compress()

◆ locally_owned_domain_indices()

◆ locally_owned_range_indices()

◆ n_nonzero_elements()

◆ get_mpi_communicator()

◆ operator const Mat &()

◆ petsc_matrix()

◆ setup_nest_mat()

◆ create_empty_matrices_if_needed()

◆ copy_from()

◆ block() [1/2]

◆ block() [2/2]

◆ m()

◆ n()

◆ n_block_rows()

◆ n_block_cols()

◆ set() [1/5]

◆ set() [2/5]

◆ set() [3/5]

◆ set() [4/5]

◆ set() [5/5]

◆ add() [1/6]

◆ add() [2/6]

◆ add() [3/6]

◆ add() [4/6]

◆ add() [5/6]

◆ add() [6/6]

◆ operator()()

◆ el()

◆ diag_element()

◆ operator*=()

◆ operator/=()

◆ vmult_add()

◆ Tvmult_add()

◆ matrix_norm_square()