#include <PETScMatrix.h>

Inheritance diagram for dolfin::PETScMatrix:

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Collaboration diagram for dolfin::PETScMatrix:

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Public Member Functions
	PETScMatrix ()
	Create empty matrix (on MPI_COMM_WORLD)

	PETScMatrix (MPI_Comm comm)
	Create empty matrix.

	PETScMatrix (Mat A)

	PETScMatrix (const PETScMatrix &A)
	Copy constructor.

virtual	~PETScMatrix ()
	Destructor.

void	init (const TensorLayout &tensor_layout)
	Initialize zero tensor using tensor layout.

bool	empty () const
	Return true if empty.

std::size_t	size (std::size_t dim) const
	Return size of given dimension.

std::pair< std::int64_t, std::int64_t >	local_range (std::size_t dim) const
	Return local ownership range.

std::size_t	nnz () const
	Return number of non-zero entries in matrix (collective)

virtual void	zero ()
	Set all entries to zero and keep any sparse structure.

virtual void	apply (std::string mode)

MPI_Comm	mpi_comm () const
	Return MPI communicator.

virtual std::string	str (bool verbose) const
	Return informal string representation (pretty-print)

virtual std::shared_ptr< GenericMatrix >	copy () const
	Return copy of matrix.

virtual void	init_vector (GenericVector &z, std::size_t dim) const

virtual void	get (double block, std::size_t m, const dolfin::la_index rows, std::size_t n, const dolfin::la_index *cols) const
	Get block of values.

virtual void	set (const double block, std::size_t m, const dolfin::la_index rows, std::size_t n, const dolfin::la_index *cols)
	Set block of values using global indices.

virtual void	set_local (const double block, std::size_t m, const dolfin::la_index rows, std::size_t n, const dolfin::la_index *cols)
	Set block of values using local indices.

virtual void	add (const double block, std::size_t m, const dolfin::la_index rows, std::size_t n, const dolfin::la_index *cols)
	Add block of values using global indices.

virtual void	add_local (const double block, std::size_t m, const dolfin::la_index rows, std::size_t n, const dolfin::la_index *cols)
	Add block of values using local indices.

virtual void	axpy (double a, const GenericMatrix &A, bool same_nonzero_pattern)
	Add multiple of given matrix (AXPY operation)

double	norm (std::string norm_type) const
	Return norm of matrix.

virtual void	getrow (std::size_t row, std::vector< std::size_t > &columns, std::vector< double > &values) const
	Get non-zero values of given row.

virtual void	setrow (std::size_t row, const std::vector< std::size_t > &columns, const std::vector< double > &values)
	Set values for given row.

virtual void	zero (std::size_t m, const dolfin::la_index *rows)
	Set given rows (global row indices) to zero.

virtual void	zero_local (std::size_t m, const dolfin::la_index *rows)
	Set given rows (local row indices) to zero.

virtual void	ident (std::size_t m, const dolfin::la_index *rows)
	Set given rows (global row indices) to identity matrix.

virtual void	ident_local (std::size_t m, const dolfin::la_index *rows)
	Set given rows (local row indices) to identity matrix.

virtual void	mult (const GenericVector &x, GenericVector &y) const
	Compute matrix-vector product y = Ax.

virtual void	transpmult (const GenericVector &x, GenericVector &y) const

virtual void	get_diagonal (GenericVector &x) const
	Get diagonal of a matrix.

virtual void	set_diagonal (const GenericVector &x)
	Set diagonal of a matrix.

virtual const PETScMatrix &	operator*= (double a)
	Multiply matrix by given number.

virtual const PETScMatrix &	operator/= (double a)
	Divide matrix by given number.

virtual const GenericMatrix &	operator= (const GenericMatrix &A)
	Assignment operator.

virtual bool	is_symmetric (double tol) const
	Test if matrix is symmetric.

virtual GenericLinearAlgebraFactory &	factory () const
	Return linear algebra backend factory.

void	set_options_prefix (std::string options_prefix)

std::string	get_options_prefix () const

void	set_from_options ()
	Call PETSc function MatSetFromOptions on the PETSc Mat object.

const PETScMatrix &	operator= (const PETScMatrix &A)
	Assignment operator.

void	set_nullspace (const VectorSpaceBasis &nullspace)

void	set_near_nullspace (const VectorSpaceBasis &nullspace)

void	binary_dump (std::string file_name) const
	Dump matrix to PETSc binary format.

Public Member Functions inherited from dolfin::GenericMatrix
virtual	~GenericMatrix ()
	Destructor.

virtual std::size_t	rank () const
	Return tensor rank (number of dimensions)

virtual void	get (double block, const dolfin::la_index num_rows, const dolfin::la_index const rows) const
	Get block of values.

virtual void	set (const double block, const dolfin::la_index num_rows, const dolfin::la_index const rows)
	Set block of values using global indices.

virtual void	set_local (const double block, const dolfin::la_index num_rows, const dolfin::la_index const rows)
	Set block of values using local indices.

virtual void	add (const double block, const dolfin::la_index num_rows, const dolfin::la_index const rows)
	Add block of values using global indices.

virtual void	add_local (const double block, const dolfin::la_index num_rows, const dolfin::la_index const rows)
	Add block of values using local indices.

virtual void	add (const double *block, const std::vector< ArrayView< const dolfin::la_index >> &rows)
	Add block of values using global indices.

virtual void	add_local (const double *block, const std::vector< ArrayView< const dolfin::la_index >> &rows)
	Add block of values using local indices.

const GenericMatrix &	operator+= (const GenericMatrix &A)
	Add given matrix.

const GenericMatrix &	operator-= (const GenericMatrix &A)
	Subtract given matrix.

virtual double	operator() (dolfin::la_index i, dolfin::la_index j) const
	Get value of given entry.

virtual double	getitem (std::pair< dolfin::la_index, dolfin::la_index > ij) const
	Get value of given entry.

virtual void	setitem (std::pair< dolfin::la_index, dolfin::la_index > ij, double value)

virtual void	ident_zeros (double tol=DOLFIN_EPS)
	Insert one on the diagonal for all zero rows.

Public Member Functions inherited from dolfin::GenericTensor
virtual	~GenericTensor ()
	Destructor.

Public Member Functions inherited from dolfin::LinearAlgebraObject
virtual const LinearAlgebraObject *	instance () const
	Return concrete instance / unwrap (const version)

virtual LinearAlgebraObject *	instance ()
	Return concrete instance / unwrap (non-const version)

virtual std::shared_ptr< const LinearAlgebraObject >	shared_instance () const
	Return concrete shared ptr instance / unwrap (const version)

virtual std::shared_ptr< LinearAlgebraObject >	shared_instance ()
	Return concrete shared ptr instance / unwrap (non-const version)

Public Member Functions inherited from dolfin::Variable
	Variable ()
	Create unnamed variable.

	Variable (const std::string name, const std::string label)
	Create variable with given name and label.

	Variable (const Variable &variable)
	Copy constructor.

virtual	~Variable ()
	Destructor.

const Variable &	operator= (const Variable &variable)
	Assignment operator.

void	rename (const std::string name, const std::string label)
	Rename variable.

std::string	name () const
	Return name.

std::string	label () const
	Return label (description)

std::size_t	id () const

Public Member Functions inherited from dolfin::PETScBaseMatrix
	PETScBaseMatrix ()
	Constructor.

	PETScBaseMatrix (Mat A)
	Constructor.

	PETScBaseMatrix (const PETScBaseMatrix &A)
	Copy constructor.

	~PETScBaseMatrix ()
	Destructor.

std::size_t	size (std::size_t dim) const
	Return number of rows (dim = 0) or columns (dim = 1)

std::pair< std::int64_t, std::int64_t >	size () const

std::pair< std::int64_t, std::int64_t >	local_range (std::size_t dim) const
	Return local range along dimension dim.

void	init_vector (GenericVector &z, std::size_t dim) const

Mat	mat () const
	Return PETSc Mat pointer.

MPI_Comm	mpi_comm () const
	Return the MPI communicator.

Public Member Functions inherited from dolfin::PETScObject
	PETScObject ()
	Constructor. Ensures that PETSc has been initialised.

virtual	~PETScObject ()
	Destructor.

Additional Inherited Members
Static Public Member Functions inherited from dolfin::PETScObject
static void	petsc_error (int error_code, std::string filename, std::string petsc_function)
	Print error message for PETSc calls that return an error.

Public Attributes inherited from dolfin::Variable
Parameters	parameters
	Parameters.

Protected Member Functions inherited from dolfin::GenericLinearOperator
virtual void	init_layout (const GenericVector &x, const GenericVector &y, GenericLinearOperator *wrapper)

Protected Attributes inherited from dolfin::PETScBaseMatrix
Mat	_matA

Detailed Description

This class provides a simple matrix class based on PETSc. It is a wrapper for a PETSc matrix pointer (Mat) implementing the GenericMatrix interface.

The interface is intentionally simple. For advanced usage, access the PETSc Mat pointer using the function mat() and use the standard PETSc interface.

Constructor & Destructor Documentation

◆ PETScMatrix()

PETScMatrix::PETScMatrix ( Mat A )

explicit

Create a wrapper around a PETSc Mat pointer. The Mat object should have been created, e.g. via PETSc MatCreate.

Member Function Documentation

◆ apply()

void PETScMatrix::apply ( std::string mode )

virtual

Finalize assembly of tensor. The following values are recognized for the mode parameter:

add - corresponds to PETSc MatAssemblyBegin+End(MAT_FINAL_ASSEMBLY) insert - corresponds to PETSc MatAssemblyBegin+End(MAT_FINAL_ASSEMBLY) flush - corresponds to PETSc MatAssemblyBegin+End(MAT_FLUSH_ASSEMBLY)

Implements dolfin::GenericMatrix.

◆ get_options_prefix()

std::string PETScMatrix::get_options_prefix ( ) const

Returns the prefix used by PETSc when searching the options database

◆ init_vector()

virtual void dolfin::PETScMatrix::init_vector	(	GenericVector &	z,
		std::size_t	dim
	)		const

inlinevirtual

Initialize vector z to be compatible with the matrix-vector product y = Ax. In the parallel case, both size and layout are important.

Parameters

z	(GenericVector&) Vector to initialise
dim	(std::size_t) The dimension (axis): dim = 0 –> z = y, dim = 1 –> z = x

Implements dolfin::GenericMatrix.

◆ set_near_nullspace()

void PETScMatrix::set_near_nullspace ( const VectorSpaceBasis & nullspace )

Attach near nullspace to matrix (used by preconditioners, such as smoothed aggregation algerbraic multigrid)

◆ set_nullspace()

void PETScMatrix::set_nullspace ( const VectorSpaceBasis & nullspace )

Attach nullspace to matrix (typically used by Krylov solvers when solving singular systems)

◆ set_options_prefix()

void PETScMatrix::set_options_prefix ( std::string options_prefix )

Sets the prefix used by PETSc when searching the options database

◆ transpmult()

void PETScMatrix::transpmult	(	const GenericVector &	x,
		GenericVector &	y
	)		const

virtual

Matrix-vector product, y = A^T x. The y vector must either be zero-sized or have correct size and parallel layout.

Implements dolfin::GenericMatrix.

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

/home/fenics/shared/dolfin/dolfin/la/PETScMatrix.h
/home/fenics/shared/dolfin/dolfin/la/PETScMatrix.cpp

Public Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ PETScMatrix()

Member Function Documentation

◆ apply()

◆ get_options_prefix()

◆ init_vector()

◆ set_near_nullspace()

◆ set_nullspace()

◆ set_options_prefix()

◆ transpmult()