This class creates and provides basic support for the Mat matrix object type used in PETSc. More...

#include <PetscMatrix.hpp>

Inheritance diagram for geos::PetscMatrix:

Public Types
using	Vector = PetscVector
	Compatible vector type.

using	Export = PetscExport
	Associated exporter type.

using	Mat = struct _p_Mat *
	Alias for PETSc matrix struct pointer.

Public Types inherited from geos::LinearOperator< PetscVector >
using	Vector = PetscVector
	Alias for template parameter.

Public Member Functions
const Mat &	unwrapped () const
	Returns a const pointer to the underlying matrix. More...

Mat &	unwrapped ()
	Returns a non-const pointer to the underlying matrix. More...

Constructor/Destructor Methods
	PetscMatrix ()
	Empty matrix constructor.

	PetscMatrix (PetscMatrix const &src)
	Copy constructor. More...

	PetscMatrix (PetscMatrix &&src) noexcept
	Move constructor. More...

PetscMatrix &	operator= (PetscMatrix const &src)
	Copy assignment. More...

PetscMatrix &	operator= (PetscMatrix &&src) noexcept
	Move assignment. More...

	~PetscMatrix () override
	Destructor.

MatrixBase interface
virtual void	createWithLocalSize (localIndex const localRows, localIndex const localCols, localIndex const maxEntriesPerRow, MPI_Comm const &comm) override
	Create a rectangular matrix from number of rows/columns. More...

virtual void	createWithGlobalSize (globalIndex const globalRows, globalIndex const globalCols, localIndex const maxEntriesPerRow, MPI_Comm const &comm) override
	Create a rectangular matrix from number of rows/columns. More...

virtual bool	created () const override
	Get the number of global rows. More...

virtual void	reset () override
	Reset the matrix to default state.

virtual void	set (real64 const value) override
	Set all non-zero elements to a value. More...

virtual void	zero () override
	Set all elements to zero.

virtual void	open () override
	Open matrix for adding new entries. More...

virtual void	close () override
	Assemble and compress the matrix. More...

virtual void	add (globalIndex const rowIndex, globalIndex const colIndex, real64 const value) override
	Add to one element. More...

virtual void	set (globalIndex const rowIndex, globalIndex const colIndex, real64 const value) override
	Set one element. More...

virtual void	insert (globalIndex const rowIndex, globalIndex const colIndex, real64 const value) override
	Insert one element. More...

virtual void	add (globalIndex const rowIndex, globalIndex const colIndices, real64 const values, localIndex const size) override
	Add elements to one row using c-style arrays. More...

virtual void	set (globalIndex const rowIndex, globalIndex const colIndices, real64 const values, localIndex const size) override
	Set elements to one row using c-style arrays. More...

virtual void	insert (globalIndex const rowIndex, globalIndex const colIndices, real64 const values, localIndex const size) override
	Insert elements to one row using c-style arrays. More...

virtual void	add (globalIndex const rowIndex, arraySlice1d< globalIndex const > const &colIndices, arraySlice1d< real64 const > const &values) override
	Add elements to one row using array1d. More...

virtual void	set (globalIndex const rowIndex, arraySlice1d< globalIndex const > const &colIndices, arraySlice1d< real64 const > const &values) override
	Set elements of one row using array1d. More...

virtual void	insert (globalIndex const rowIndex, arraySlice1d< globalIndex const > const &colIndices, arraySlice1d< real64 const > const &values) override
	Insert elements of one row using array1d. More...

virtual void	add (arraySlice1d< globalIndex const > const &rowIndices, arraySlice1d< globalIndex const > const &colIndices, arraySlice2d< real64 const > const &values) override
	Add a dense block of values. More...

virtual void	set (arraySlice1d< globalIndex const > const &rowIndices, arraySlice1d< globalIndex const > const &colIndices, arraySlice2d< real64 const > const &values) override
	Set a dense block of values. More...

virtual void	insert (arraySlice1d< globalIndex const > const &rowIndices, arraySlice1d< globalIndex const > const &colIndices, arraySlice2d< real64 const > const &values) override
	Insert a dense block of values. More...

virtual void	add (globalIndex const rowIndices, globalIndex const colIndices, real64 const *values, localIndex const numRows, localIndex const numCols) override
	Add a dense block of values. More...

virtual void	set (globalIndex const rowIndices, globalIndex const colIndices, real64 const *values, localIndex const numRows, localIndex const numCols) override
	Set a dense block of values. More...

virtual void	insert (globalIndex const rowIndices, globalIndex const colIndices, real64 const *values, localIndex const numRows, localIndex const numCols) override
	Insert dense matrix. More...

virtual void	insert (arrayView1d< globalIndex const > const &rowIndices, arrayView1d< globalIndex const > const &colIndices, arrayView1d< real64 const > const &values) override
	Insert values stored in 3 linear vectors. More...

virtual void	apply (PetscVector const &src, PetscVector &dst) const override
	Apply operator to a vector, `dst = this(src)`. More...

virtual void	multiply (PetscMatrix const &src, PetscMatrix &dst) const override
	Matrix/Matrix multiplication. More...

virtual void	applyTranspose (Vector const &src, Vector &dst) const override
	Apply transpose of the matrix to a vector. More...

virtual void	leftMultiplyTranspose (PetscMatrix const &src, PetscMatrix &dst) const override
	Matrix/Matrix transpose multiplication. More...

virtual void	rightMultiplyTranspose (PetscMatrix const &src, PetscMatrix &dst) const override
	Matrix/Matrix transpose multiplication. More...

virtual void	multiplyRAP (PetscMatrix const &R, PetscMatrix const &P, PetscMatrix &dst) const override
	Compute the triple product `dst = R * this * P` More...

virtual void	multiplyPtAP (PetscMatrix const &P, PetscMatrix &dst) const override
	Compute the triple product `dst = P^T * this * P` More...

virtual void	gemv (real64 const alpha, PetscVector const &x, real64 const beta, PetscVector &y, bool useTranspose=false) const override
	Compute gemv `y = alphaAx + beta*y`. More...

virtual void	scale (real64 const scalingFactor) override
	Multiply all elements by scalingFactor. More...

virtual void	leftScale (PetscVector const &vec) override
	Pre-multiplies (left) with diagonal matrix consisting of the values in vec. More...

virtual void	rightScale (PetscVector const &vec) override
	Post-multiplies (right) with diagonal matrix consisting of the values in vec. More...

virtual void	leftRightScale (PetscVector const &vecLeft, PetscVector const &vecRight) override
	Post-multiplies (right) with diagonal matrix consisting of the values in vecRight and pre-multiplies (left) with diagonal matrix consisting of the values in vec. More...

virtual void	rescaleRows (arrayView1d< globalIndex const > const &rowIndices, RowSumType const rowSumType) override
	Rescales selected rows of matrix using row sum reciprocal as a factor. More...

virtual void	transpose (PetscMatrix &dst) const override
	Matrix transposition. More...

virtual void	separateComponentFilter (PetscMatrix &dst, integer const dofsPerNode) const override
	Apply a separate component approximation (filter) to this matrix. More...

virtual real64	clearRow (globalIndex const row, bool const keepDiag=false, real64 const diagValue=0.0) override
	Clear a row, and optionally set diagonal element to `diagValue`. More...

virtual void	addEntries (PetscMatrix const &src, MatrixPatternOp const op, real64 const scale=1.0) override
	Add entries of another matrix to this. More...

virtual void	addDiagonal (PetscVector const &src, real64 const scale) override
	Add (scaled) entries of a vector to the diagonal of this matrix. More...

virtual void	clampEntries (real64 const lo, real64 const hi, bool const excludeDiag) override
	Clamp each matrix value between values of `lo` and `hi`. More...

virtual localIndex	maxRowLength () const override
	Returns the number of nonzero entries in the longest row of the matrix. More...

virtual localIndex	rowLength (globalIndex const globalRowIndex) const override
	Get row length via global row index. More...

virtual void	getRowLengths (arrayView1d< localIndex > const &lengths) const override
	Get the row lengths of every local row. More...

virtual void	extractDiagonal (PetscVector &dst) const override
	Extract diagonal values into a vector. More...

virtual void	getRowSums (PetscVector &dst, RowSumType const rowSumType) const override
	Populate a vector with row sums of `this`. More...

virtual void	getRowCopy (globalIndex globalRow, arraySlice1d< globalIndex > const &colIndices, arraySlice1d< real64 > const &values) const override
	Returns a copy of the data in row `globalRow`. More...

virtual globalIndex	numGlobalRows () const override
	Get the number of global rows. More...

virtual globalIndex	numGlobalCols () const override
	Get the number of global columns. More...

virtual localIndex	numLocalRows () const override
	Get the number of local rows. More...

virtual localIndex	numLocalCols () const override
	Get the number of local columns. More...

virtual globalIndex	ilower () const override
	Returns the index of the first global row owned by that processor. More...

virtual globalIndex	iupper () const override
	Returns index one past the last global row owned by that processor. More...

virtual globalIndex	jlower () const override
	Returns the index of the first global col owned by that processor. More...

virtual globalIndex	jupper () const override
	Returns index one past the last global col owned by that processor. More...

virtual localIndex	numLocalNonzeros () const override
	Returns the number of nonzeros in the local portion of the matrix. More...

virtual globalIndex	numGlobalNonzeros () const override
	Returns the total number of nonzeros in the matrix. More...

virtual real64	normInf () const override
	Returns the infinity norm of the matrix. More...

virtual real64	norm1 () const override
	Returns the one norm of the matrix. More...

virtual real64	normFrobenius () const override
	Returns the Frobenius norm of the matrix. More...

virtual real64	normMax () const override
	Returns the max norm of the matrix (the largest absolute element value). More...

virtual real64	normMax (arrayView1d< globalIndex const > const &m) const override
	Returns the max norm of the matrix on a subset of rows. More...

virtual localIndex	getLocalRowID (globalIndex const index) const override
	Map a global row index to local row index. More...

virtual globalIndex	getGlobalRowID (localIndex const index) const override
	Map a local row index to global row index. More...

virtual MPI_Comm	comm () const override
	Get the MPI communicator the matrix was created with. More...

virtual void	print (std::ostream &os=std::cout) const override
	Print the matrix in Trilinos format to a stream. More...

virtual void	write (string const &filename, LAIOutputFormat const format=LAIOutputFormat::MATRIX_MARKET) const override
	Write the matrix to filename in a matlab-compatible format. More...

virtual void	createWithLocalSize (localIndex const localSize, localIndex const maxEntriesPerRow, MPI_Comm const &comm)
	Create a square matrix from local number of rows. More...

virtual void	createWithLocalSize (localIndex const localRows, localIndex const localCols, localIndex const maxEntriesPerRow, MPI_Comm const &comm)=0
	Create a rectangular matrix from number of rows/columns. More...

virtual void	createWithGlobalSize (globalIndex const globalSize, localIndex const maxEntriesPerRow, MPI_Comm const &comm)
	Create a square matrix from global number of rows. More...

virtual void	createWithGlobalSize (globalIndex const globalRows, globalIndex const globalCols, localIndex const maxEntriesPerRow, MPI_Comm const &comm)=0
	Create a rectangular matrix from number of rows/columns. More...

virtual void	create (CRSMatrixView< real64 const, globalIndex const > const &localMatrix, localIndex const numLocalColumns, MPI_Comm const &comm)
	Create parallel matrix from a local CRS matrix. More...

bool	closed () const
	Query matrix closed status. More...

bool	assembled () const
	Query matrix assembled status. More...

bool	insertable () const
	Query matrix status. More...

bool	modifiable () const
	Query matrix status. More...

bool	ready () const
	Query matrix ready status. More...

virtual void	residual (Vector const &x, Vector const &b, Vector &r) const override
	Compute residual `r = b - A * x`. More...

void	setDofManager (DofManager const *const dofManager)
	Associate a DofManager with this matrix. More...

DofManager const *	dofManager () const

Public Member Functions inherited from geos::LinearOperator< PetscVector >
	LinearOperator ()=default
	Constructor.

virtual	~LinearOperator ()=default
	Destructor.

Detailed Description

This class creates and provides basic support for the Mat matrix object type used in PETSc.

Definition at line 49 of file PetscMatrix.hpp.

Constructor & Destructor Documentation

◆ PetscMatrix() [1/2]

geos::PetscMatrix::PetscMatrix ( PetscMatrix const & src )

Copy constructor.

Parameters

[in] src the matrix to be copied

◆ PetscMatrix() [2/2]

geos::PetscMatrix::PetscMatrix ( PetscMatrix && src )

noexcept

Move constructor.

Parameters

[in] src the matrix to be copied

Member Function Documentation

◆ add() [1/5]

virtual void geos::PetscMatrix::add	(	arraySlice1d< globalIndex const > const &	rowIndices,
		arraySlice1d< globalIndex const > const &	colIndices,
		arraySlice2d< real64 const > const &	values
	)

overridevirtual

Add a dense block of values.

Parameters

rowIndices	Global row indices
colIndices	Global col indices
values	Dense local matrix of values

Implements geos::MatrixBase< PetscMatrix, PetscVector >.

◆ add() [2/5]

virtual void geos::PetscMatrix::add	(	globalIndex const *	rowIndices,
		globalIndex const *	colIndices,
		real64 const *	values,
		localIndex const	numRows,
		localIndex const	numCols
	)

overridevirtual

Add a dense block of values.

Parameters

rowIndices	Global row indices
colIndices	Global col indices
values	Dense local matrix of values
numRows	Number of row indices
numCols	Number of column indices

Note: Row major layout assumed in values

Implements geos::MatrixBase< PetscMatrix, PetscVector >.

◆ add() [3/5]

virtual void geos::PetscMatrix::add	(	globalIndex const	rowIndex,
		arraySlice1d< globalIndex const > const &	colIndices,
		arraySlice1d< real64 const > const &	values
	)

overridevirtual

Add elements to one row using array1d.

Parameters

rowIndex	Global row index
colIndices	Global column indices
values	Values to add to prescribed locations

Implements geos::MatrixBase< PetscMatrix, PetscVector >.

◆ add() [4/5]

virtual void geos::PetscMatrix::add	(	globalIndex const	rowIndex,
		globalIndex const *	colIndices,
		real64 const *	values,
		localIndex const	size
	)

overridevirtual

Add elements to one row using c-style arrays.

Parameters

rowIndex	Global row index
colIndices	Global column indices
values	Values to add to prescribed locations
size	Number of elements

Implements geos::MatrixBase< PetscMatrix, PetscVector >.

◆ add() [5/5]

virtual void geos::PetscMatrix::add	(	globalIndex const	rowIndex,
		globalIndex const	colIndex,
		real64 const	value
	)

overridevirtual

Add to one element.

Parameters

rowIndex	Global row index
colIndex	Global column index
value	Value to add to prescribed location

Implements geos::MatrixBase< PetscMatrix, PetscVector >.

◆ addDiagonal()

virtual void geos::PetscMatrix::addDiagonal	(	PetscVector const &	src,
		real64 const	scale
	)

overridevirtual

Add (scaled) entries of a vector to the diagonal of this matrix.

Parameters

src	the source vector
scale	optional scaling factor

Note: this must be square and have a (possibly zero) diagonal entry in every row. this and src must have the same parallel row distribution.

Implements geos::MatrixBase< PetscMatrix, PetscVector >.

◆ addEntries()

virtual void geos::PetscMatrix::addEntries	(	PetscMatrix const &	src,
		MatrixPatternOp const	op,
		real64 const	scale = `1.0`
	)

overridevirtual

Add entries of another matrix to this.

Parameters

src	the source matrix
op	handling of nonzero patterns, see MatrixPatternOp
scale	factor to scale entries of `src` by

Note: Sparsity pattern of this must be a superset of sparsity of src. this and src must have the same parallel row distribution.

Implements geos::MatrixBase< PetscMatrix, PetscVector >.

◆ apply()

virtual void geos::PetscMatrix::apply	(	PetscVector const &	src,
		PetscVector &	dst
	)		const

overridevirtual

Apply operator to a vector, dst = this(src).

Parameters

src	input vector
dst	output vector

Warning: src and dst cannot alias the same vector (some implementations may allow this).

Implements geos::LinearOperator< PetscVector >.

◆ applyTranspose()

virtual void geos::PetscMatrix::applyTranspose	(	Vector const &	src,
		Vector &	dst
	)		const

overridevirtual

Apply transpose of the matrix to a vector.

Parameters

src	Input vector (x).
dst	Output vector (b).

Implements geos::MatrixBase< PetscMatrix, PetscVector >.

◆ assembled()

bool geos::MatrixBase< MATRIX, VECTOR >::assembled

inline

Query matrix assembled status.

Returns: true if matrix has been opened and closed since creation; false otherwise

Definition at line 108 of file MatrixBase.hpp.

◆ clampEntries()

virtual void geos::PetscMatrix::clampEntries	(	real64 const	lo,
		real64 const	hi,
		bool const	excludeDiag
	)

overridevirtual

Clamp each matrix value between values of lo and hi.

Parameters

lo	min value
hi	max value
excludeDiag	iff `true`, diagonal values are unchanged

Effectively sets each matrix value v to min(max(v, lo), hi).

Implements geos::MatrixBase< PetscMatrix, PetscVector >.

◆ clearRow()

virtual real64 geos::PetscMatrix::clearRow	(	globalIndex const	row,
		bool const	keepDiag = `false`,
		real64 const	diagValue = `0.0`
	)

overridevirtual

Clear a row, and optionally set diagonal element to diagValue.

Parameters

row	globalIndex of the row to be cleared.
diagValue	(Optional) set diagonal element to desired value.
keepDiag	if `true`, `diagValue` is ignored and original diagonal is preserved

Returns: original diagonal value if matrix is square; zero otherwise

Note: diagValue and keepDiag are ignored if the matrix is not square

Implements geos::MatrixBase< PetscMatrix, PetscVector >.

◆ close()

virtual void geos::PetscMatrix::close ( )

overridevirtual

Assemble and compress the matrix.

Compresses the matrix to CSR format with contiguous memory on each processor. Prevents from adding new entries in the sparsity pattern but allows for modification of existing entries.

Implements geos::MatrixBase< PetscMatrix, PetscVector >.

◆ closed()

bool geos::MatrixBase< MATRIX, VECTOR >::closed

inline

Query matrix closed status.

Returns: true if matrix has been opened and has not been closed since; false otherwise

Definition at line 102 of file MatrixBase.hpp.

◆ comm()

virtual MPI_Comm geos::PetscMatrix::comm ( ) const

overridevirtual

Get the MPI communicator the matrix was created with.

Returns: MPI communicator passed in create...()

Note: when build without MPI, may return anything (MPI_Comm will be a mock type defined in MpiWrapper)

Implements geos::LinearOperator< PetscVector >.

◆ create()

virtual void geos::MatrixBase< MATRIX, VECTOR >::create

inline

Create parallel matrix from a local CRS matrix.

Parameters

localMatrix	The input local matrix.
numLocalColumns	number of local columns (not available from localMatrix in general)
comm	The MPI communicator to use.

Note: Copies values, so that localMatrix does not need to retain its values after the call.

Todo:: Replace generic implementation with more efficient ones in each package.

Definition at line 248 of file MatrixBase.hpp.

◆ created()

virtual bool geos::PetscMatrix::created ( ) const

overridevirtual

Get the number of global rows.

Returns: Number of global rows in the operator.

Implements geos::MatrixBase< PetscMatrix, PetscVector >.

◆ createWithGlobalSize() [1/3]

virtual void geos::PetscMatrix::createWithGlobalSize	(	globalIndex const	globalRows,
		globalIndex const	globalCols,
		localIndex const	maxEntriesPerRow,
		MPI_Comm const &	comm
	)

overridevirtual

Create a rectangular matrix from number of rows/columns.

Parameters

comm	MPI communicator.
globalRows	Global number of rows.
globalCols	Global number of columns.
maxEntriesPerRow	Maximum number of entries per row (hint).

Implements geos::MatrixBase< PetscMatrix, PetscVector >.

◆ createWithGlobalSize() [2/3]

virtual void geos::MatrixBase< MATRIX, VECTOR >::createWithGlobalSize

Create a rectangular matrix from number of rows/columns.

Parameters

comm	MPI communicator.
globalRows	Global number of rows.
globalCols	Global number of columns.
maxEntriesPerRow	Maximum number of entries per row (hint).

◆ createWithGlobalSize() [3/3]

virtual void geos::MatrixBase< MATRIX, VECTOR >::createWithGlobalSize

inline

Create a square matrix from global number of rows.

Create a square matrix with an (approximately) even partitioning of rows.

Parameters

globalSize	Global dimensions for a square matrix.
maxEntriesPerRow	Maximum number of non-zero entries per row.
comm	MPI communicator.

Definition at line 204 of file MatrixBase.hpp.

◆ createWithLocalSize() [1/3]

virtual void geos::PetscMatrix::createWithLocalSize	(	localIndex const	localRows,
		localIndex const	localCols,
		localIndex const	maxEntriesPerRow,
		MPI_Comm const &	comm
	)

overridevirtual

Create a rectangular matrix from number of rows/columns.

Parameters

comm	MPI communicator.
localRows	Local number of rows.
localCols	Local number of columns.
maxEntriesPerRow	Maximum number of entries per row (hint).

Implements geos::MatrixBase< PetscMatrix, PetscVector >.

◆ createWithLocalSize() [2/3]

virtual void geos::MatrixBase< MATRIX, VECTOR >::createWithLocalSize

Create a rectangular matrix from number of rows/columns.

Parameters

comm	MPI communicator.
localRows	Local number of rows.
localCols	Local number of columns.
maxEntriesPerRow	Maximum number of entries per row (hint).

◆ createWithLocalSize() [3/3]

virtual void geos::MatrixBase< MATRIX, VECTOR >::createWithLocalSize

inline

Create a square matrix from local number of rows.

Parameters

localSize	local number of rows for square matrix.
maxEntriesPerRow	Maximum number of non-zero entries per row.
comm	MPI communicator.

Definition at line 186 of file MatrixBase.hpp.

◆ dofManager()

DofManager const* geos::MatrixBase< MATRIX, VECTOR >::dofManager

inline

Returns: the associated DofManager

Definition at line 165 of file MatrixBase.hpp.

◆ extractDiagonal()

virtual void geos::PetscMatrix::extractDiagonal ( PetscVector & dst ) const

overridevirtual

Extract diagonal values into a vector.

Parameters

dst	the target vector, must have the same row partitioning as `this`

Implements geos::MatrixBase< PetscMatrix, PetscVector >.

◆ gemv()

virtual void geos::PetscMatrix::gemv	(	real64 const	alpha,
		PetscVector const &	x,
		real64 const	beta,
		PetscVector &	y,
		bool	useTranspose = `false`
	)		const

overridevirtual

Compute gemv y = alpha*A*x + beta*y.

Note: The naming convention follows the BLAS library.

Parameters

alpha	Scalar factor for added matvec product.
x	Input vector.
beta	Scalar factor for right hand side.
y	Output vector.
useTranspose	Boolean, set to true to use `A^T`.

Warning: x and y cannot alias the same vector.

Implements geos::MatrixBase< PetscMatrix, PetscVector >.

◆ getGlobalRowID()

virtual globalIndex geos::PetscMatrix::getGlobalRowID ( localIndex const index ) const

overridevirtual

Map a local row index to global row index.

Parameters

index the local row index (between 0 and number of local rows)

Returns: the global row index corresponding to index

Implements geos::MatrixBase< PetscMatrix, PetscVector >.

◆ getLocalRowID()

virtual localIndex geos::PetscMatrix::getLocalRowID ( globalIndex const index ) const

overridevirtual

Map a global row index to local row index.

Parameters

index the global row index

Returns: the local row index corresponding to index, or -1 if not a local row

Implements geos::MatrixBase< PetscMatrix, PetscVector >.

◆ getRowCopy()

virtual void geos::PetscMatrix::getRowCopy	(	globalIndex	globalRow,
		arraySlice1d< globalIndex > const &	colIndices,
		arraySlice1d< real64 > const &	values
	)		const

overridevirtual

Returns a copy of the data in row globalRow.

Parameters

[in]	globalRow	the index of global row to extract
[out]	colIndices	the output array of global column indices (must have a large enough size)
[out]	values	the output array of values (must have a large enough size)

Implements geos::MatrixBase< PetscMatrix, PetscVector >.

◆ getRowLengths()

virtual void geos::PetscMatrix::getRowLengths ( arrayView1d< localIndex > const & lengths ) const

overridevirtual

Get the row lengths of every local row.

Parameters

lengths an array view to be populated with row lengths

Note: The implementation may move the view's buffer to a different memory space.

Implements geos::MatrixBase< PetscMatrix, PetscVector >.

◆ getRowSums()

virtual void geos::PetscMatrix::getRowSums	(	PetscVector &	dst,
		RowSumType const	rowSumType
	)		const

overridevirtual

Populate a vector with row sums of this.

Parameters

dst	the target vector, must have the same row partitioning as `this`
rowSumType	type of row sum operation to perform

Implements geos::MatrixBase< PetscMatrix, PetscVector >.

◆ ilower()

virtual globalIndex geos::PetscMatrix::ilower ( ) const

overridevirtual

Returns the index of the first global row owned by that processor.

Returns: the index of the first global row owned by that processor

Implements geos::MatrixBase< PetscMatrix, PetscVector >.

◆ insert() [1/6]

virtual void geos::PetscMatrix::insert	(	arraySlice1d< globalIndex const > const &	rowIndices,
		arraySlice1d< globalIndex const > const &	colIndices,
		arraySlice2d< real64 const > const &	values
	)

overridevirtual

Insert a dense block of values.

Parameters

rowIndices	Global row indices
colIndices	Global col indices
values	Dense local matrix of values

Implements geos::MatrixBase< PetscMatrix, PetscVector >.

◆ insert() [2/6]

virtual void geos::PetscMatrix::insert	(	arrayView1d< globalIndex const > const &	rowIndices,
		arrayView1d< globalIndex const > const &	colIndices,
		arrayView1d< real64 const > const &	values
	)

overridevirtual

Insert values stored in 3 linear vectors.

Parameters

rowIndices	Array of global row indices
colIndices	Array of global column indices
values	Array of values

Implements geos::MatrixBase< PetscMatrix, PetscVector >.

◆ insert() [3/6]

virtual void geos::PetscMatrix::insert	(	globalIndex const *	rowIndices,
		globalIndex const *	colIndices,
		real64 const *	values,
		localIndex const	numRows,
		localIndex const	numCols
	)

overridevirtual

Insert dense matrix.

Parameters

rowIndices	Global row indices
colIndices	Global col indices
values	Dense local matrix of values
numRows	Number of row indices
numCols	Number of column indices

Note: Row major layout assumed in values

Implements geos::MatrixBase< PetscMatrix, PetscVector >.

◆ insert() [4/6]

virtual void geos::PetscMatrix::insert	(	globalIndex const	rowIndex,
		arraySlice1d< globalIndex const > const &	colIndices,
		arraySlice1d< real64 const > const &	values
	)

overridevirtual

Insert elements of one row using array1d.

Parameters

rowIndex	Global row index
colIndices	Global column indices
values	Values to add to prescribed locations

Implements geos::MatrixBase< PetscMatrix, PetscVector >.

◆ insert() [5/6]

virtual void geos::PetscMatrix::insert	(	globalIndex const	rowIndex,
		globalIndex const *	colIndices,
		real64 const *	values,
		localIndex const	size
	)

overridevirtual

Insert elements to one row using c-style arrays.

Parameters

rowIndex	Global row index
colIndices	Global column indices
values	Values to add to prescribed locations
size	Number of elements

Implements geos::MatrixBase< PetscMatrix, PetscVector >.

◆ insert() [6/6]

virtual void geos::PetscMatrix::insert	(	globalIndex const	rowIndex,
		globalIndex const	colIndex,
		real64 const	value
	)

overridevirtual

Insert one element.

Parameters

rowIndex	Global row index
colIndex	Global column index
value	Value to insert at prescribed location

Implements geos::MatrixBase< PetscMatrix, PetscVector >.

◆ insertable()

bool geos::MatrixBase< MATRIX, VECTOR >::insertable

inline

Query matrix status.

Returns: true if matrix has NOT been assembled yet (not closed since last create() call) and is currently open for insertion of new entries

Definition at line 130 of file MatrixBase.hpp.

◆ iupper()

virtual globalIndex geos::PetscMatrix::iupper ( ) const

overridevirtual

Returns index one past the last global row owned by that processor.

Returns: the next index after last global row owned by that processor

Note: The intention is for [ilower; iupper) to be used as a half-open index range

Implements geos::MatrixBase< PetscMatrix, PetscVector >.

◆ jlower()

virtual globalIndex geos::PetscMatrix::jlower ( ) const

overridevirtual

Returns the index of the first global col owned by that processor.

Returns: index of the first owned global col

Note: Matrix implementations don't physically "own" column ranges the same way they do row ranges. Instead, the column range refers to the "diagonal" block of columns which would correspond to the local range of entries of a vector created with the same local/global size as the number of matrix columns.

Implements geos::MatrixBase< PetscMatrix, PetscVector >.

◆ jupper()

virtual globalIndex geos::PetscMatrix::jupper ( ) const

overridevirtual

Returns index one past the last global col owned by that processor.

Returns: index one past the last owned global col

Note: The intention is for [jlower; jupper) to be used as a half-open index range.; Also see note for jlower() about the meaning of "owned" columns.

Implements geos::MatrixBase< PetscMatrix, PetscVector >.

◆ leftMultiplyTranspose()

virtual void geos::PetscMatrix::leftMultiplyTranspose	(	PetscMatrix const &	src,
		PetscMatrix &	dst
	)		const

overridevirtual

Matrix/Matrix transpose multiplication.

Compute this^T * B = C.

Parameters

src	Input matrix (B).
dst	Output matrix (C).

Note: The output matrix dst doesn't need to be created beforehand.

Implements geos::MatrixBase< PetscMatrix, PetscVector >.

◆ leftRightScale()

virtual void geos::PetscMatrix::leftRightScale	(	PetscVector const &	vecLeft,
		PetscVector const &	vecRight
	)

overridevirtual

Post-multiplies (right) with diagonal matrix consisting of the values in vecRight and pre-multiplies (left) with diagonal matrix consisting of the values in vec.

Parameters

vecLeft	vec to pre-multiply with.
vecRight	vec to post-multiply with.

Implements geos::MatrixBase< PetscMatrix, PetscVector >.

◆ leftScale()

virtual void geos::PetscMatrix::leftScale ( PetscVector const & vec )

overridevirtual

Pre-multiplies (left) with diagonal matrix consisting of the values in vec.

Parameters

vec	Vector to pre-multiply with.

Implements geos::MatrixBase< PetscMatrix, PetscVector >.

◆ maxRowLength()

virtual localIndex geos::PetscMatrix::maxRowLength ( ) const

overridevirtual

Returns the number of nonzero entries in the longest row of the matrix.

Returns: the max length of a row

Collective.

Implements geos::MatrixBase< PetscMatrix, PetscVector >.

◆ modifiable()

bool geos::MatrixBase< MATRIX, VECTOR >::modifiable

inline

Query matrix status.

Returns: true if matrix has been assembled and is currently open; this implies individual entries within existing sparsity pattern can be altered via set()/add() methods.

Definition at line 123 of file MatrixBase.hpp.

◆ multiply()

virtual void geos::PetscMatrix::multiply	(	PetscMatrix const &	src,
		PetscMatrix &	dst
	)		const

overridevirtual

Matrix/Matrix multiplication.

Compute this * B = C.

Parameters

src	Input matrix (B).
dst	Output matrix (C).

Note: The output matrix dst doesn't need to be created beforehand.

Implements geos::MatrixBase< PetscMatrix, PetscVector >.

◆ multiplyPtAP()

virtual void geos::PetscMatrix::multiplyPtAP	(	PetscMatrix const &	P,
		PetscMatrix &	dst
	)		const

overridevirtual

Compute the triple product dst = P^T * this * P

Parameters

P	the "prolongation" matrix
dst	the resulting product matrix (will be re-created as needed)

Reimplemented from geos::MatrixBase< PetscMatrix, PetscVector >.

◆ multiplyRAP()

virtual void geos::PetscMatrix::multiplyRAP	(	PetscMatrix const &	R,
		PetscMatrix const &	P,
		PetscMatrix &	dst
	)		const

overridevirtual

Compute the triple product dst = R * this * P

Parameters

R	the "restriction" matrix
P	the "prolongation" matrix
dst	the resulting product matrix (will be re-created as needed)

Reimplemented from geos::MatrixBase< PetscMatrix, PetscVector >.

◆ norm1()

virtual real64 geos::PetscMatrix::norm1 ( ) const

overridevirtual

Returns the one norm of the matrix.

Returns: the value of 1-norm

Implements geos::MatrixBase< PetscMatrix, PetscVector >.

◆ normFrobenius()

virtual real64 geos::PetscMatrix::normFrobenius ( ) const

overridevirtual

Returns the Frobenius norm of the matrix.

Returns: the value of Frobenius norm

Implements geos::MatrixBase< PetscMatrix, PetscVector >.

◆ normInf()

virtual real64 geos::PetscMatrix::normInf ( ) const

overridevirtual

Returns the infinity norm of the matrix.

Returns: the value of infinity norm

Implements geos::MatrixBase< PetscMatrix, PetscVector >.

◆ normMax() [1/2]

virtual real64 geos::PetscMatrix::normMax ( ) const

overridevirtual

Returns the max norm of the matrix (the largest absolute element value).

Returns: the value of max norm

Implements geos::MatrixBase< PetscMatrix, PetscVector >.

◆ normMax() [2/2]

virtual real64 geos::PetscMatrix::normMax ( arrayView1d< globalIndex const > const & rowIndices ) const

overridevirtual

Returns the max norm of the matrix on a subset of rows.

Parameters

rowIndices global indices of rows to compute norm over

Returns: the value of max norm

Implements geos::MatrixBase< PetscMatrix, PetscVector >.

◆ numGlobalCols()

virtual globalIndex geos::PetscMatrix::numGlobalCols ( ) const

overridevirtual

Get the number of global columns.

Returns: Number of global columns in the operator.

Implements geos::LinearOperator< PetscVector >.

◆ numGlobalNonzeros()

virtual globalIndex geos::PetscMatrix::numGlobalNonzeros ( ) const

overridevirtual

Returns the total number of nonzeros in the matrix.

Returns: the total number of nonzeros in the matrix

Implements geos::MatrixBase< PetscMatrix, PetscVector >.

◆ numGlobalRows()

virtual globalIndex geos::PetscMatrix::numGlobalRows ( ) const

overridevirtual

Get the number of global rows.

Returns: Number of global rows in the operator.

Implements geos::LinearOperator< PetscVector >.

◆ numLocalCols()

virtual localIndex geos::PetscMatrix::numLocalCols ( ) const

overridevirtual

Get the number of local columns.

Returns: Number of local columns in the operator.

Note: The use of term "local columns" refers not to physical partitioning of columns across ranks (as e.g. matrices are partitioned by rows and typically physically store all column entries), but to the partitioning of a compatible vector object that this operator can be applied to.

Implements geos::LinearOperator< PetscVector >.

◆ numLocalNonzeros()

virtual localIndex geos::PetscMatrix::numLocalNonzeros ( ) const

overridevirtual

Returns the number of nonzeros in the local portion of the matrix.

Returns: the number of nonzeros in the local portion of the matrix

Implements geos::MatrixBase< PetscMatrix, PetscVector >.

◆ numLocalRows()

virtual localIndex geos::PetscMatrix::numLocalRows ( ) const

overridevirtual

Get the number of local rows.

Returns: Number of local rows in the operator.

Implements geos::LinearOperator< PetscVector >.

◆ open()

virtual void geos::PetscMatrix::open ( )

overridevirtual

Open matrix for adding new entries.

Note: Adding entries that result in modifications of sparsity pattern may not be allowed by most implementations. An error will be raised in that case.

Implements geos::MatrixBase< PetscMatrix, PetscVector >.

◆ operator=() [1/2]

PetscMatrix& geos::PetscMatrix::operator= ( PetscMatrix && src )

noexcept

Move assignment.

Parameters

src	matrix to be moved from.

Returns: the new matrix.

◆ operator=() [2/2]

PetscMatrix& geos::PetscMatrix::operator= ( PetscMatrix const & src )

Copy assignment.

Parameters

src	matrix to be copied.

Returns: the new vector.

◆ print()

virtual void geos::PetscMatrix::print ( std::ostream & os = std::cout ) const

overridevirtual

Print the matrix in Trilinos format to a stream.

Parameters

os	the output stream

Implements geos::MatrixBase< PetscMatrix, PetscVector >.

◆ ready()

bool geos::MatrixBase< MATRIX, VECTOR >::ready

inline

Query matrix ready status.

Returns: true if matrix has been assembled and is currently closed; this implies it's ready to be used or re-opened for adding/setting values

Definition at line 115 of file MatrixBase.hpp.

◆ rescaleRows()

virtual void geos::PetscMatrix::rescaleRows	(	arrayView1d< globalIndex const > const &	rowIndices,
		RowSumType const	rowSumType
	)

overridevirtual

Rescales selected rows of matrix using row sum reciprocal as a factor.

Parameters

rowIndices	global indicies of rows to scale (all must be locally owned)
rowSumType	type of row sums to use as scaling factors

Implements geos::MatrixBase< PetscMatrix, PetscVector >.

◆ residual()

virtual void geos::MatrixBase< MATRIX, VECTOR >::residual

inlineoverride

Compute residual r = b - A * x.

Overrides LinearOperator::residual().

Parameters

x	Input solution.
b	Input right hand side.
r	Output residual.

Warning: x and r cannot alias the same vector, but b and r can.

Definition at line 551 of file MatrixBase.hpp.

◆ rightMultiplyTranspose()

virtual void geos::PetscMatrix::rightMultiplyTranspose	(	PetscMatrix const &	src,
		PetscMatrix &	dst
	)		const

overridevirtual

Matrix/Matrix transpose multiplication.

Compute B * this^T = C.

Parameters

src	Input matrix (B).
dst	Output matrix (C).

Note: The output matrix dst doesn't need to be created beforehand.

Implements geos::MatrixBase< PetscMatrix, PetscVector >.

◆ rightScale()

virtual void geos::PetscMatrix::rightScale ( PetscVector const & vec )

overridevirtual

Post-multiplies (right) with diagonal matrix consisting of the values in vec.

Parameters

vec	Vector to post-multiply with.

Implements geos::MatrixBase< PetscMatrix, PetscVector >.

◆ rowLength()

virtual localIndex geos::PetscMatrix::rowLength ( globalIndex const globalRowIndex ) const

overridevirtual

Get row length via global row index.

Parameters

[in] globalRowIndex the global row index

Returns: the number of nonzero entries in the row

Implements geos::MatrixBase< PetscMatrix, PetscVector >.

◆ scale()

virtual void geos::PetscMatrix::scale ( real64 const scalingFactor )

overridevirtual

Multiply all elements by scalingFactor.

Parameters

scalingFactor Scaling factor.

Implements geos::MatrixBase< PetscMatrix, PetscVector >.

◆ separateComponentFilter()

virtual void geos::PetscMatrix::separateComponentFilter	(	PetscMatrix &	dst,
		integer const	dofPerPoint
	)		const

overridevirtual

Apply a separate component approximation (filter) to this matrix.

Parameters

dst	the target (filtered) matrix
dofPerPoint	number of degrees-of-freedom per node

Implements geos::MatrixBase< PetscMatrix, PetscVector >.

◆ set() [1/6]

virtual void geos::PetscMatrix::set	(	arraySlice1d< globalIndex const > const &	rowIndices,
		arraySlice1d< globalIndex const > const &	colIndices,
		arraySlice2d< real64 const > const &	values
	)

overridevirtual

Set a dense block of values.

Parameters

rowIndices	Global row indices
colIndices	Global col indices
values	Dense local matrix of values

Implements geos::MatrixBase< PetscMatrix, PetscVector >.

◆ set() [2/6]

virtual void geos::PetscMatrix::set	(	globalIndex const *	rowIndices,
		globalIndex const *	colIndices,
		real64 const *	values,
		localIndex const	numRows,
		localIndex const	numCols
	)

overridevirtual

Set a dense block of values.

Parameters

rowIndices	Global row indices
colIndices	Global col indices
values	Dense local matrix of values
numRows	Number of row indices
numCols	Number of column indices

Note: Row major layout assumed in values

Implements geos::MatrixBase< PetscMatrix, PetscVector >.

◆ set() [3/6]

virtual void geos::PetscMatrix::set	(	globalIndex const	rowIndex,
		arraySlice1d< globalIndex const > const &	colIndices,
		arraySlice1d< real64 const > const &	values
	)

overridevirtual

Set elements of one row using array1d.

Parameters

rowIndex	Global row index
colIndices	Global column indices
values	Values to add to prescribed locations

Implements geos::MatrixBase< PetscMatrix, PetscVector >.

◆ set() [4/6]

virtual void geos::PetscMatrix::set	(	globalIndex const	rowIndex,
		globalIndex const *	colIndices,
		real64 const *	values,
		localIndex const	size
	)

overridevirtual

Set elements to one row using c-style arrays.

Parameters

rowIndex	Global row index
colIndices	Global column indices
values	Values to add to prescribed locations
size	Number of elements

Implements geos::MatrixBase< PetscMatrix, PetscVector >.

◆ set() [5/6]

virtual void geos::PetscMatrix::set	(	globalIndex const	rowIndex,
		globalIndex const	colIndex,
		real64 const	value
	)

overridevirtual

Set one element.

Parameters

rowIndex	Global row index
colIndex	Global column index
value	Value to set at prescribed location

Implements geos::MatrixBase< PetscMatrix, PetscVector >.

◆ set() [6/6]

virtual void geos::PetscMatrix::set ( real64 const value )

overridevirtual

Set all non-zero elements to a value.

Parameters

value the value to set all elements to

Implements geos::MatrixBase< PetscMatrix, PetscVector >.

◆ setDofManager()

void geos::MatrixBase< MATRIX, VECTOR >::setDofManager

inline

Associate a DofManager with this matrix.

Parameters

dofManager the DofManager containing the relevant degrees of freedom

Definition at line 157 of file MatrixBase.hpp.

◆ transpose()

virtual void geos::PetscMatrix::transpose ( PetscMatrix & dst ) const

overridevirtual

Matrix transposition.

Compute B = this^T.

Parameters

dst	Output matrix (B).

Implements geos::MatrixBase< PetscMatrix, PetscVector >.

◆ unwrapped() [1/2]

Mat& geos::PetscMatrix::unwrapped ( )

Returns a non-const pointer to the underlying matrix.

Returns: the non-const pointer to the underlying matrix.

◆ unwrapped() [2/2]

const Mat& geos::PetscMatrix::unwrapped ( ) const

Returns a const pointer to the underlying matrix.

Returns: the const pointer to the underlying matrix.

◆ write()

virtual void geos::PetscMatrix::write	(	string const &	filename,
		LAIOutputFormat const	format = `LAIOutputFormat::MATRIX_MARKET`
	)		const

overridevirtual

Write the matrix to filename in a matlab-compatible format.

Parameters

filename	name of the output file
format	output format

Within octave / matlab:

load filename M = spconvert(filename_root)

Implements geos::MatrixBase< PetscMatrix, PetscVector >.

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

coreComponents/linearAlgebra/interfaces/petsc/PetscMatrix.hpp

Public Types

Public Member Functions

Detailed Description

Constructor & Destructor Documentation

◆ PetscMatrix() [1/2]

◆ PetscMatrix() [2/2]

Member Function Documentation

◆ add() [1/5]

◆ add() [2/5]

◆ add() [3/5]

◆ add() [4/5]

◆ add() [5/5]

◆ addDiagonal()

◆ addEntries()

◆ apply()

◆ applyTranspose()

◆ assembled()

◆ clampEntries()

◆ clearRow()

◆ close()

◆ closed()

◆ comm()

◆ create()

◆ created()

◆ createWithGlobalSize() [1/3]

◆ createWithGlobalSize() [2/3]

◆ createWithGlobalSize() [3/3]

◆ createWithLocalSize() [1/3]

◆ createWithLocalSize() [2/3]

◆ createWithLocalSize() [3/3]

◆ dofManager()

◆ extractDiagonal()

◆ gemv()

◆ getGlobalRowID()

◆ getLocalRowID()

◆ getRowCopy()

◆ getRowLengths()

◆ getRowSums()

◆ ilower()

◆ insert() [1/6]

◆ insert() [2/6]

◆ insert() [3/6]

◆ insert() [4/6]

◆ insert() [5/6]

◆ insert() [6/6]

◆ insertable()

◆ iupper()

◆ jlower()

◆ jupper()

◆ leftMultiplyTranspose()

◆ leftRightScale()

◆ leftScale()

◆ maxRowLength()

◆ modifiable()

◆ multiply()

◆ multiplyPtAP()

◆ multiplyRAP()

◆ norm1()

◆ normFrobenius()

◆ normInf()

◆ normMax() [1/2]

◆ normMax() [2/2]

◆ numGlobalCols()

◆ numGlobalNonzeros()

◆ numGlobalRows()

◆ numLocalCols()

◆ numLocalNonzeros()

◆ numLocalRows()

◆ open()

◆ operator=() [1/2]

◆ operator=() [2/2]

◆ print()

◆ ready()

◆ rescaleRows()

◆ residual()

◆ rightMultiplyTranspose()

◆ rightScale()

◆ rowLength()

◆ scale()

◆ separateComponentFilter()