Wrapper for PETSc's matrix class. More...

#include <petsc.hpp>

Inheritance diagram for mfem::PetscParMatrix:

Collaboration diagram for mfem::PetscParMatrix:

Public Member Functions
	PetscParMatrix ()
	Create an empty matrix to be used as a reference to an existing matrix. More...

	PetscParMatrix (Mat a, bool ref=false)
	Creates PetscParMatrix out of PETSc's Mat. More...

	PetscParMatrix (const PetscParMatrix *pa, Operator::Type tid)
	Convert a PetscParMatrix pa with a new PETSc format tid. Note that if pa is already a PetscParMatrix of the same type as tid, the resulting PetscParMatrix will share the same Mat object. More...

	PetscParMatrix (const PetscParMatrix &A, const mfem::Array< PetscInt > &rows, const mfem::Array< PetscInt > &cols)
	Creates a PetscParMatrix extracting the submatrix of A with rows row indices and cols column indices. More...

	PetscParMatrix (const HypreParMatrix *ha, Operator::Type tid=Operator::PETSC_MATAIJ)
	Convert a HypreParMatrix ha to a PetscParMatrix in the given PETSc format tid. More...

	PetscParMatrix (const SparseMatrix *sa, Operator::Type tid=Operator::PETSC_MATAIJ)
	Convert a SparseMatrix ha to a PetscParMatrix in the given PETSc format tid. More...

	PetscParMatrix (MPI_Comm comm, const Operator *op, Operator::Type tid=Operator::PETSC_MATSHELL)
	Convert an mfem::Operator into a PetscParMatrix in the given PETSc format tid. More...

	PetscParMatrix (MPI_Comm comm, PetscInt glob_size, PetscInt row_starts, SparseMatrix diag, Operator::Type tid)
	Creates block-diagonal square parallel matrix. More...

	PetscParMatrix (MPI_Comm comm, PetscInt global_num_rows, PetscInt global_num_cols, PetscInt row_starts, PetscInt col_starts, SparseMatrix *diag, Operator::Type tid)
	Creates block-diagonal rectangular parallel matrix. More...

virtual	~PetscParMatrix ()
	Calls PETSc's destroy function. More...

void	SetMat (Mat newA)
	Replace the inner Mat Object. The reference count of newA is increased. More...

void	Mult (double a, const Vector &x, double b, Vector &y) const
	Matvec: y = a A x + b y. More...

void	MultTranspose (double a, const Vector &x, double b, Vector &y) const
	Matvec transpose: y = a A^T x + b y. More...

virtual void	Mult (const Vector &x, Vector &y) const
	Operator application: `y=A(x)`. More...

virtual void	MultTranspose (const Vector &x, Vector &y) const
	Action of the transpose operator: `y=A^t(x)`. The default behavior in class Operator is to generate an error. More...

MPI_Comm	GetComm () const
	Get the associated MPI communicator. More...

	operator Mat () const
	Typecasting to PETSc's Mat type. More...

	operator PetscObject () const
	Typecasting to PETSc object. More...

PetscInt	GetRowStart () const
	Returns the global index of the first local row. More...

PetscInt	GetColStart () const
	Returns the global index of the first local column. More...

PetscInt	GetNumRows () const
	Returns the local number of rows. More...

PetscInt	GetNumCols () const
	Returns the local number of columns. More...

PetscInt	M () const
	Returns the global number of rows. More...

PetscInt	N () const
	Returns the global number of columns. More...

PetscInt	GetGlobalNumRows () const
	Returns the global number of rows. More...

PetscInt	GetGlobalNumCols () const
	Returns the global number of columns. More...

PetscInt	NNZ () const
	Returns the number of nonzeros. More...

PetscParVector *	GetX () const
	Returns the inner vector in the domain of A (it creates it if needed) More...

PetscParVector *	GetY () const
	Returns the inner vector in the range of A (it creates it if needed) More...

PetscParMatrix *	Transpose (bool action=false)
	Returns the transpose of the PetscParMatrix. More...

void	Print (const char *fname=NULL, bool binary=false) const
	Prints the matrix (to stdout if fname is NULL) More...

void	operator*= (double s)
	Scale all entries by s: A_scaled = s*A. More...

void	EliminateRowsCols (const Array< int > &rows_cols, const PetscParVector &X, PetscParVector &B, double diag=1.)
	Eliminate rows and columns from the matrix, and rows from the vector B. Modify B with the BC values in X. Put diag on the diagonal corresponding to eliminated entries. More...

void	EliminateRowsCols (const Array< int > &rows_cols, const HypreParVector &X, HypreParVector &B, double diag=1.)

PetscParMatrix *	EliminateRowsCols (const Array< int > &rows_cols)
	Eliminate rows and columns from the matrix and store the eliminated elements in a new matrix Ae (returned). More...

void	ScaleRows (const Vector &s)
	Scale the local row i by s(i). More...

void	ScaleCols (const Vector &s)
	Scale the local col i by s(i). More...

void	Shift (double s)
	Shift diagonal by a constant. More...

void	Shift (const Vector &s)
	Shift diagonal by a vector. More...

void	EliminateRows (const Array< int > &rows)
	Eliminate only the rows from the matrix. More...

void	MakeRef (const PetscParMatrix &master)
	Makes this object a reference to another PetscParMatrix. More...

Mat	ReleaseMat (bool dereference)
	Release the PETSc Mat object. If dereference is true, decrement the refcount of the Mat object. More...

Type	GetType () const

Assignment operators
PetscParMatrix &	operator= (const PetscParMatrix &B)

PetscParMatrix &	operator= (const HypreParMatrix &B)

PetscParMatrix &	operator+= (const PetscParMatrix &B)

PetscParMatrix &	operator-= (const PetscParMatrix &B)

Public Member Functions inherited from mfem::Operator
	Operator (int s=0)
	Construct a square Operator with given size s (default 0). More...

	Operator (int h, int w)
	Construct an Operator with the given height (output size) and width (input size). More...

int	Height () const
	Get the height (size of output) of the Operator. Synonym with NumRows(). More...

int	NumRows () const
	Get the number of rows (size of output) of the Operator. Synonym with Height(). More...

int	Width () const
	Get the width (size of input) of the Operator. Synonym with NumCols(). More...

int	NumCols () const
	Get the number of columns (size of input) of the Operator. Synonym with Width(). More...

virtual MemoryClass	GetMemoryClass () const
	Return the MemoryClass preferred by the Operator. More...

virtual Operator &	GetGradient (const Vector &x) const
	Evaluate the gradient operator at the point x. The default behavior in class Operator is to generate an error. More...

virtual const Operator *	GetProlongation () const
	Prolongation operator from linear algebra (linear system) vectors, to input vectors for the operator. `NULL` means identity. More...

virtual const Operator *	GetRestriction () const
	Restriction operator from input vectors for the operator to linear algebra (linear system) vectors. `NULL` means identity. More...

void	FormLinearSystem (const Array< int > &ess_tdof_list, Vector &x, Vector &b, Operator *&A, Vector &X, Vector &B, int copy_interior=0)
	Form a constrained linear system using a matrix-free approach. More...

virtual void	RecoverFEMSolution (const Vector &X, const Vector &b, Vector &x)
	Reconstruct a solution vector x (e.g. a GridFunction) from the solution X of a constrained linear system obtained from Operator::FormLinearSystem(). More...

void	PrintMatlab (std::ostream &out, int n=0, int m=0) const
	Prints operator with input size n and output size m in Matlab format. More...

virtual	~Operator ()
	Virtual destructor. More...

Type	GetType () const
	Return the type ID of the Operator class. More...

Protected Member Functions
void	Init ()
	Initialize with defaults. Does not initialize inherited members. More...

void	Destroy ()
	Delete all owned data. Does not perform re-initialization with defaults. More...

void	MakeWrapper (MPI_Comm comm, const Operator op, Mat B)
	Creates a wrapper around a mfem::Operator op using PETSc's MATSHELL object and returns the Mat in B. More...

void	ConvertOperator (MPI_Comm comm, const Operator &op, Mat *B, Operator::Type tid)

Protected Attributes
Mat	A
	The actual PETSc object. More...

PetscParVector *	X
	Auxiliary vectors for typecasting. More...

PetscParVector *	Y

Protected Attributes inherited from mfem::Operator
int	height
	Dimension of the output / number of rows in the matrix. More...

int	width
	Dimension of the input / number of columns in the matrix. More...

Friends
class	PetscLinearSolver

class	PetscPreconditioner

Additional Inherited Members
Public Types inherited from mfem::Operator
enum	Type { ANY_TYPE, MFEM_SPARSEMAT, Hypre_ParCSR, PETSC_MATAIJ, PETSC_MATIS, PETSC_MATSHELL, PETSC_MATNEST, PETSC_MATHYPRE, PETSC_MATGENERIC }
	Enumeration defining IDs for some classes derived from Operator. More...

Detailed Description

Wrapper for PETSc's matrix class.

Definition at line 196 of file petsc.hpp.

Constructor & Destructor Documentation

mfem::PetscParMatrix::PetscParMatrix ( )

Create an empty matrix to be used as a reference to an existing matrix.

Definition at line 533 of file petsc.cpp.

mfem::PetscParMatrix::PetscParMatrix	(	Mat	a,
		bool	ref = `false`
	)

Creates PetscParMatrix out of PETSc's Mat.

Parameters

[in]	a	The PETSc Mat object.
[in]	ref	If true, we increase the reference count of a.

Definition at line 1246 of file petsc.cpp.

mfem::PetscParMatrix::PetscParMatrix	(	const PetscParMatrix *	pa,
		Operator::Type	tid
	)

explicit

Convert a PetscParMatrix pa with a new PETSc format tid. Note that if pa is already a PetscParMatrix of the same type as tid, the resulting PetscParMatrix will share the same Mat object.

Definition at line 558 of file petsc.cpp.

mfem::PetscParMatrix::PetscParMatrix	(	const PetscParMatrix &	A,
		const mfem::Array< PetscInt > &	rows,
		const mfem::Array< PetscInt > &	cols
	)

Creates a PetscParMatrix extracting the submatrix of A with rows row indices and cols column indices.

Definition at line 538 of file petsc.cpp.

mfem::PetscParMatrix::PetscParMatrix	(	const HypreParMatrix *	ha,
		Operator::Type	tid = `Operator::PETSC_MATAIJ`
	)

explicit

Convert a HypreParMatrix ha to a PetscParMatrix in the given PETSc format tid.

The supported type ids are: Operator::PETSC_MATAIJ, Operator::PETSC_MATIS, Operator::PETSC_MATSHELL and Operator::PETSC_MATHYPRE ha can be destroyed unless tid == PETSC_MATSHELL or tid == PETSC_MATHYPRE

Definition at line 566 of file petsc.cpp.

mfem::PetscParMatrix::PetscParMatrix	(	const SparseMatrix *	sa,
		Operator::Type	tid = `Operator::PETSC_MATAIJ`
	)

explicit

Convert a SparseMatrix ha to a PetscParMatrix in the given PETSc format tid.

Definition at line 574 of file petsc.cpp.

mfem::PetscParMatrix::PetscParMatrix	(	MPI_Comm	comm,
		const Operator *	op,
		Operator::Type	tid = `Operator::PETSC_MATSHELL`
	)

Convert an mfem::Operator into a PetscParMatrix in the given PETSc format tid.

If tid is Operator::PETSC_MATSHELL and op is not a PetscParMatrix, it converts any mfem::Operator op implementing Operator::Mult() and Operator::MultTranspose() into a PetscParMatrix. The Operator op should not be deleted while the constructed PetscParMatrix is used.

Otherwise, it tries to convert the operator in PETSc's classes. op cannot be destroyed if tid == PETSC_MATHYPRE.

In particular, if op is a BlockOperator, then a MATNEST Mat object is created using tid as the type for the blocks. Note that if op is already a PetscParMatrix of the same type as tid, the resulting PetscParMatrix will share the same Mat object

Definition at line 582 of file petsc.cpp.

mfem::PetscParMatrix::PetscParMatrix	(	MPI_Comm	comm,
		PetscInt	glob_size,
		PetscInt *	row_starts,
		SparseMatrix *	diag,
		Operator::Type	tid
	)

Creates block-diagonal square parallel matrix.

The block-diagonal is given by diag which must be in CSR format (finalized). The new PetscParMatrix does not take ownership of any of the input arrays. The type id tid can be either PETSC_MATAIJ (parallel distributed CSR) or PETSC_MATIS.

Definition at line 591 of file petsc.cpp.

mfem::PetscParMatrix::PetscParMatrix	(	MPI_Comm	comm,
		PetscInt	global_num_rows,
		PetscInt	global_num_cols,
		PetscInt *	row_starts,
		PetscInt *	col_starts,
		SparseMatrix *	diag,
		Operator::Type	tid
	)

Creates block-diagonal rectangular parallel matrix.

The block-diagonal is given by diag which must be in CSR format (finalized). The new PetscParMatrix does not take ownership of any of the input arrays. The type id tid can be either PETSC_MATAIJ (parallel distributed CSR) or PETSC_MATIS.

Definition at line 603 of file petsc.cpp.

virtual mfem::PetscParMatrix::~PetscParMatrix ( )

inlinevirtual

Calls PETSc's destroy function.

Definition at line 304 of file petsc.hpp.

Member Function Documentation

void mfem::PetscParMatrix::ConvertOperator	(	MPI_Comm	comm,
		const Operator &	op,
		Mat *	B,
		Operator::Type	tid
	)

protected

Convert an mfem::Operator into a Mat B; op can be destroyed unless tid == PETSC_MATSHELL or tid == PETSC_MATHYPRE if op is a BlockOperator, the operator type is relevant to the individual blocks

Definition at line 854 of file petsc.cpp.

void mfem::PetscParMatrix::Destroy ( )

protected

Delete all owned data. Does not perform re-initialization with defaults.

Definition at line 1233 of file petsc.cpp.

void mfem::PetscParMatrix::EliminateRows ( const Array< int > & rows )

Eliminate only the rows from the matrix.

Definition at line 1648 of file petsc.cpp.

void mfem::PetscParMatrix::EliminateRowsCols	(	const Array< int > &	rows_cols,
		const PetscParVector &	X,
		PetscParVector &	B,
		double	diag = `1.`
	)

Eliminate rows and columns from the matrix, and rows from the vector B. Modify B with the BC values in X. Put diag on the diagonal corresponding to eliminated entries.

Definition at line 1619 of file petsc.cpp.

void mfem::PetscParMatrix::EliminateRowsCols	(	const Array< int > &	rows_cols,
		const HypreParVector &	X,
		HypreParVector &	B,
		double	diag = `1.`
	)

Definition at line 1611 of file petsc.cpp.

PetscParMatrix * mfem::PetscParMatrix::EliminateRowsCols ( const Array< int > & rows_cols )

Eliminate rows and columns from the matrix and store the eliminated elements in a new matrix Ae (returned).

The sum of the modified matrix and the returned matrix, Ae, is equal to the original matrix.

Definition at line 1600 of file petsc.cpp.

PetscInt mfem::PetscParMatrix::GetColStart ( ) const

Returns the global index of the first local column.

Definition at line 484 of file petsc.cpp.

MPI_Comm mfem::PetscParMatrix::GetComm ( ) const

Get the associated MPI communicator.

Definition at line 820 of file petsc.cpp.

PetscInt mfem::PetscParMatrix::GetGlobalNumCols ( ) const

inline

Returns the global number of columns.

Definition at line 360 of file petsc.hpp.

PetscInt mfem::PetscParMatrix::GetGlobalNumRows ( ) const

inline

Returns the global number of rows.

Definition at line 357 of file petsc.hpp.

PetscInt mfem::PetscParMatrix::GetNumCols ( ) const

Returns the local number of columns.

Definition at line 498 of file petsc.cpp.

PetscInt mfem::PetscParMatrix::GetNumRows ( ) const

Returns the local number of rows.

Definition at line 491 of file petsc.cpp.

PetscInt mfem::PetscParMatrix::GetRowStart ( ) const

Returns the global index of the first local row.

Definition at line 477 of file petsc.cpp.

Operator::Type mfem::PetscParMatrix::GetType ( ) const

Definition at line 1675 of file petsc.cpp.

PetscParVector * mfem::PetscParMatrix::GetX ( ) const

Returns the inner vector in the domain of A (it creates it if needed)

Definition at line 1336 of file petsc.cpp.

PetscParVector * mfem::PetscParMatrix::GetY ( ) const

Returns the inner vector in the range of A (it creates it if needed)

Definition at line 1346 of file petsc.cpp.

void mfem::PetscParMatrix::Init ( )

protected

Initialize with defaults. Does not initialize inherited members.

Definition at line 526 of file petsc.cpp.

PetscInt mfem::PetscParMatrix::M ( ) const

Returns the global number of rows.

Definition at line 505 of file petsc.cpp.

void mfem::PetscParMatrix::MakeRef ( const PetscParMatrix & master )

Makes this object a reference to another PetscParMatrix.

Definition at line 1326 of file petsc.cpp.

void mfem::PetscParMatrix::MakeWrapper	(	MPI_Comm	comm,
		const Operator *	op,
		Mat *	B
	)

protected

Creates a wrapper around a mfem::Operator op using PETSc's MATSHELL object and returns the Mat in B.

This does not take any reference to op, that should not be destroyed until B is needed.

Definition at line 833 of file petsc.cpp.

void mfem::PetscParMatrix::Mult	(	double	a,
		const Vector &	x,
		double	b,
		Vector &	y
	)		const

Matvec: y = a A x + b y.

Definition at line 1375 of file petsc.cpp.

virtual void mfem::PetscParMatrix::Mult	(	const Vector &	x,
		Vector &	y
	)		const

inlinevirtual

Operator application: y=A(x).

Implements mfem::Operator.

Definition at line 323 of file petsc.hpp.

void mfem::PetscParMatrix::MultTranspose	(	double	a,
		const Vector &	x,
		double	b,
		Vector &	y
	)		const

Matvec transpose: y = a A^T x + b y.

Definition at line 1391 of file petsc.cpp.

virtual void mfem::PetscParMatrix::MultTranspose	(	const Vector &	x,
		Vector &	y
	)		const

inlinevirtual

Action of the transpose operator: y=A^t(x). The default behavior in class Operator is to generate an error.

Reimplemented from mfem::Operator.

Definition at line 326 of file petsc.hpp.

PetscInt mfem::PetscParMatrix::N ( ) const

Returns the global number of columns.

Definition at line 512 of file petsc.cpp.

PetscInt mfem::PetscParMatrix::NNZ ( ) const

Returns the number of nonzeros.

Differently from HYPRE, this call is collective on the communicator, as this number is not stored inside PETSc, but needs to be computed.

Definition at line 519 of file petsc.cpp.

mfem::PetscParMatrix::operator Mat ( ) const

inline

Typecasting to PETSc's Mat type.

Definition at line 333 of file petsc.hpp.

mfem::PetscParMatrix::operator PetscObject ( ) const

inline

Typecasting to PETSc object.

Definition at line 336 of file petsc.hpp.

void mfem::PetscParMatrix::operator*= ( double s )

Scale all entries by s: A_scaled = s*A.

Definition at line 1370 of file petsc.cpp.

PetscParMatrix & mfem::PetscParMatrix::operator+= ( const PetscParMatrix & B )

Definition at line 652 of file petsc.cpp.

PetscParMatrix & mfem::PetscParMatrix::operator-= ( const PetscParMatrix & B )

Definition at line 667 of file petsc.cpp.

PetscParMatrix & mfem::PetscParMatrix::operator= ( const PetscParMatrix & B )

Definition at line 636 of file petsc.cpp.

PetscParMatrix & mfem::PetscParMatrix::operator= ( const HypreParMatrix & B )

Definition at line 616 of file petsc.cpp.

void mfem::PetscParMatrix::Print	(	const char *	fname = `NULL`,
		bool	binary = `false`
	)		const

Prints the matrix (to stdout if fname is NULL)

Definition at line 1408 of file petsc.cpp.

Mat mfem::PetscParMatrix::ReleaseMat ( bool dereference )

Release the PETSc Mat object. If dereference is true, decrement the refcount of the Mat object.

Definition at line 1662 of file petsc.cpp.

void mfem::PetscParMatrix::ScaleCols ( const Vector & s )

Scale the local col i by s(i).

Definition at line 1444 of file petsc.cpp.

void mfem::PetscParMatrix::ScaleRows ( const Vector & s )

Scale the local row i by s(i).

Definition at line 1433 of file petsc.cpp.

void mfem::PetscParMatrix::SetMat ( Mat newA )

Replace the inner Mat Object. The reference count of newA is increased.

Definition at line 1258 of file petsc.cpp.

void mfem::PetscParMatrix::Shift ( double s )

Shift diagonal by a constant.

Definition at line 1455 of file petsc.cpp.

void mfem::PetscParMatrix::Shift ( const Vector & s )

Shift diagonal by a vector.

Definition at line 1460 of file petsc.cpp.

PetscParMatrix * mfem::PetscParMatrix::Transpose ( bool action = false )

Returns the transpose of the PetscParMatrix.

If action is false, the new matrix is constructed with the PETSc function MatTranspose(). If action is true, then the matrix is not actually transposed. Instead, an object that behaves like the transpose is returned.

Definition at line 1356 of file petsc.cpp.

Friends And Related Function Documentation

friend class PetscLinearSolver

friend

Definition at line 225 of file petsc.hpp.

friend class PetscPreconditioner

friend

Definition at line 226 of file petsc.hpp.

Member Data Documentation

Mat mfem::PetscParMatrix::A

protected

The actual PETSc object.

Definition at line 200 of file petsc.hpp.

PetscParVector* mfem::PetscParMatrix::X

mutableprotected

Auxiliary vectors for typecasting.

Definition at line 203 of file petsc.hpp.

PetscParVector * mfem::PetscParMatrix::Y

mutableprotected

Definition at line 203 of file petsc.hpp.

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

linalg/petsc.hpp
linalg/petsc.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Friends

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation