Class for representing the system matrix in PETSc format. More...

#include <PETScMatrix.h>

Inheritance diagram for PETScMatrix:

Collaboration diagram for PETScMatrix:

[legend]

Public Member Functions
	PETScMatrix (const ProcessAdm &padm, const LinSolParams &spar)
	Constructor.

	~PETScMatrix () override
	The destructor frees the dynamically allocated arrays.

LinAlg::MatrixType	getType () const override
	Returns the matrix type.

SystemMatrix *	copy () const override
	Creates a copy of the system matrix and returns a pointer to it.

size_t	dim (int idim=1) const override
	Returns the dimension of the system matrix. More...

bool	init (int maxEq, const IntMat elms=nullptr, const IntMat neighs=nullptr, const IntVec *part=nullptr)
	Initializes a scalar matrix based on element connections. More...

void	preAssemble (const std::vector< IntVec > &MMNPC, size_t nel) override
	Initializes the equation sparsity pattern based on element connections. More...

void	initAssembly (const SAM &sam, char) override
	Initializes the element assembly process. More...

void	init () override
	Initializes the matrix to zero assuming it is properly dimensioned.

bool	assemble (const Matrix &eM, const SAM &sam, int e) override
	Adds an element matrix into the associated system matrix. More...

bool	assemble (const Matrix &eM, const SAM &sam, SystemVector &B, int e) override
	Adds an element matrix into the associated system matrix. More...

bool	assemble (const Matrix &eM, const SAM &sam, SystemVector &B, const IntVec &meq) override
	Adds an element matrix into the associated system matrix. More...

bool	assemble (const Matrix &eM, const IntVec &meq) override
	Adds an element matrix into the associated system matrix. More...

bool	endAssembly () override
	Finalizes the system matrix assembly.

bool	multiply (const SystemVector &B, SystemVector &C) const override
	Performs the matrix-vector multiplication C = this B.

bool	solve (SystemVector &B, Real *) override
	Solves the linear system of equations for a given right-hand-side. More...

bool	solve (const SystemVector &B, SystemVector &x) override
	Solves the linear system of equations for a given right-hand-side. More...

void	mult (Real alpha) override
	Multiplication with a scalar.

bool	solveEig (PETScMatrix &B, RealArray &eigVal, Matrix &eigVec, int nev, Real shift=Real(0), int iop=1)
	Solves a generalized symmetric-definite eigenproblem. More...

Real	Linfnorm () const override
	Returns the L-infinity norm of the matrix.

Mat &	getMatrix ()
	Returns the PETSc matrix (for assignment).

const Mat &	getMatrix () const
	Returns the PETSc matrix (for read access).

const std::vector< Mat > &	getBlockMatrices () const
	Get vector of block matrices. Used for tests only.

const std::vector< IS > &	getIS () const
	Get vector of index sets.

bool	setParameters (bool setup)
	Set the linear solver parameters (solver type, preconditioner, tolerances). More...

const ProcessAdm &	getAdm () const
	Returns a const-ref to process administrator.

bool	solveMultipleRhs (PETScVectors &B, Matrix &sField)
	Solve for multiple right-hand-side vectors. More...

const DomainDecomposition &	getDD () const
	Returns a const-ref to domain decompositioning.

bool	add (Real sigma, int ieq) override
	Adds the constant σ to the diagonal of this matrix.

Public Member Functions inherited from SystemMatrix
virtual	~SystemMatrix ()
	Empty destructor.

virtual bool	lockPattern (bool)
	Locks or unlocks the sparsity pattern.

virtual bool	empty () const
	Checks if the matrix is empty.

bool	isZero () const
	Checks if the matrix have no non-zero contributions.

virtual void	compressPattern ()
	Compresses the sparsity pattern.

void	initNonZeroEqs ()
	Initializes the nonZeroEqs flags.

bool	flagNonZeroEqs (const IntVec &meq={})
	Flags the equations meq as pivots with non-zero contributions.

bool	flagNonZeroEqs (const SystemMatrix &B)
	Flags the non-zero equations from B as non-zero pivots in this.

virtual bool	augment (const SystemMatrix &, size_t, size_t)
	Augments a similar matrix symmetrically to the current matrix.

virtual bool	truncate (Real=Real(1.0e-16))
	Truncates all small matrix elements to zero.

virtual bool	add (const SystemMatrix &, Real=Real(1))
	Adds a matrix with similar structure to the current matrix.

virtual void	dump (std::ostream &, LinAlg::StorageFormat, const char *=nullptr)
	Dumps the system matrix on a specified format.

virtual void	dump (const char *fileName, std::streamsize precision=0, LinAlg::StorageFormat format=LinAlg::FLAT)
	Dumps the system matrix to specified file.

virtual bool	load (const char *, bool=false)
	Loads the system matrix from specified file.

StdVector	operator* (const SystemVector &b) const
	Calculates a matrix-vector product.

StdVector	operator/ (const SystemVector &b)
	Solves a linear equation system.

Protected Member Functions
bool	solve (const Vec &b, Vec &x, bool knoll)
	Solve a linear system.

	PETScMatrix (const PETScMatrix &A)=delete
	Disabled copy constructor.

	PETScMatrix (const ProcessAdm &padm, const PETScSolParams &spar)
	Clone matrix data.

void	setupSparsity (const IntVec &elms, const SAM &sam)
	Setup sparsity pattern for model. More...

void	setupBlockSparsity (const IntVec &elms, const SAM &sam)
	Setup sparsity pattern for block-matrices for a model.

void	setupGlb2Blk (const SAM &sam)
	Calculates blocks for global eqs.

Mat	preAllocator (const int nrows, const int ncols=0) const
	Sets up preallocator matrix.

std::vector< Mat >	preAllocators () const
	Sets up preallocator matrices for blocks.

Protected Member Functions inherited from SystemMatrix
	SystemMatrix ()
	Default constructor.

	SystemMatrix (const SystemMatrix &a)
	Copy constructor.

virtual std::ostream &	write (std::ostream &os) const
	Writes the system matrix to the given output stream.

Protected Attributes
Mat	pA
	The actual PETSc matrix.

PetscInt	nrow
	Number of matrix rows.

PetscInt	ncol
	Number of matrix columns.

KSP	ksp
	Linear equation solver.

MatNullSpace *	nsp
	Null-space of linear operator.

const ProcessAdm &	adm
	Process administrator.

PETScSolParams	solParams
	Linear solver parameters.

bool	setParams
	If linear solver parameters are set.

std::string	forcedKSPType
	Force a KSP type ignoring the parameters.

PetscInt	ISsize
	Number of index sets/elements.

PetscRealVec	coords
	Coordinates of local nodes (x0,y0,z0,x1,y1,...)

ISMat	dirIndexSet
	Direction ordering.

int	nLinSolves
	Number of linear solves.

bool	assembled
	True if PETSc matrix has been assembled.

bool	factored
	True if PETsc matrix has been factored.

IS	glob2LocEq = nullptr
	Index set for global-to-local equations.

std::vector< Mat >	matvec
	Blocks for block matrices.

std::vector< IS >	isvec
	Index sets for blocks.

std::vector< std::array< int, 2 > >	glb2Blk
	Maps equations to block and block eq.

std::unique_ptr< DomainDecomposition >	m_dd {}
	Internal partitioning information.

Additional Inherited Members
Static Public Member Functions inherited from SystemMatrix
static SystemMatrix *	create (const ProcessAdm *adm, LinAlg::MatrixType mType, int num_thread_SLU=1)
	Static method creating a matrix of the given type.

static SystemMatrix *	create (const ProcessAdm *adm, LinAlg::MatrixType mType, const LinSolParams &spar)
	Static method creating a matrix of the given type.

Detailed Description

Class for representing the system matrix in PETSc format.

It is an interface to PETSc modules for assembling and solving linear systems of equations.

Member Function Documentation

◆ assemble() [1/4]

bool PETScMatrix::assemble	(	const Matrix &	eM,
		const IntVec &	meq
	)

overridevirtual

Adds an element matrix into the associated system matrix.

Parameters

[in]	eM	The element matrix
[in]	meq	Matrix of element equation numbers

Returns: true on successful assembly, otherwise false

Implements SystemMatrix.

References m_dd, and pA.

◆ assemble() [2/4]

bool PETScMatrix::assemble	(	const Matrix &	eM,
		const SAM &	sam,
		int	e
	)

overridevirtual

Adds an element matrix into the associated system matrix.

Parameters

[in]	eM	The element matrix
[in]	sam	Auxiliary data for FE assembly management
[in]	e	Identifier for the element that eM belongs to

Returns: true on successful assembly, otherwise false

Implements SystemMatrix.

References adm, ProcessAdm::dd, SystemMatrix::flagNonZeroEqs(), SAM::getElmEqns(), glb2Blk, SAM::meqn, SAM::mmceq, SAM::mpmceq, utl::matrix< T >::rows(), and SAM::ttcc.

◆ assemble() [3/4]

bool PETScMatrix::assemble	(	const Matrix &	eM,
		const SAM &	sam,
		SystemVector &	B,
		const IntVec &	meq
	)

overridevirtual

Adds an element matrix into the associated system matrix.

Parameters

[in]	eM	The element matrix
[in]	sam	Auxiliary data for FE assembly management
	B	The system right-hand-side vector
[in]	meq	Matrix of element equation numbers

Returns: true on successful assembly, otherwise false

When multi-point constraints are present, contributions from these are also added into the system right-hand-side vector, B.

Implements SystemMatrix.

References adm, utl::matrix< T >::cols(), ProcessAdm::dd, SystemMatrix::flagNonZeroEqs(), glb2Blk, SAM::meqn, SAM::mmceq, SAM::mpmceq, utl::matrix< T >::rows(), and SAM::ttcc.

◆ assemble() [4/4]

bool PETScMatrix::assemble	(	const Matrix &	eM,
		const SAM &	sam,
		SystemVector &	B,
		int	e
	)

overridevirtual

Adds an element matrix into the associated system matrix.

Parameters

[in]	eM	The element matrix
[in]	sam	Auxiliary data for FE assembly management
	B	The system right-hand-side vector
[in]	e	Identifier for the element that eM belongs to

Returns: true on successful assembly, otherwise false

When multi-point constraints are present, contributions from these are also added into the system right-hand-side vector, B.

Implements SystemMatrix.

References adm, ProcessAdm::dd, SystemMatrix::flagNonZeroEqs(), SAM::getElmEqns(), glb2Blk, SAM::meqn, SAM::mmceq, SAM::mpmceq, utl::matrix< T >::rows(), and SAM::ttcc.

◆ dim()

size_t PETScMatrix::dim ( int idim = 1 ) const

overridevirtual

Returns the dimension of the system matrix.

Parameters

[in] idim Which direction to return the dimension in.

Implements SystemMatrix.

References ncol, and nrow.

Referenced by _eig_ax(), and eig_sol_().

◆ init()

bool PETScMatrix::init	(	int	maxEq,
		const IntMat *	elms = `nullptr`,
		const IntMat *	neighs = `nullptr`,
		const IntVec *	part = `nullptr`
	)

Initializes a scalar matrix based on element connections.

Parameters

[in]	maxEq	Maximum equation number
[in]	elms	Element nodal connection
[in]	neighs	Element graph
[in]	part	Partitioning to use

References adm, ProcessAdm::dd, DomainDecomposition::isPartitioned(), m_dd, ncol, nrow, and pA.

Referenced by ASMbase::globalL2projection().

◆ initAssembly()

void PETScMatrix::initAssembly	(	const SAM &	sam,
		char
	)

overridevirtual

Initializes the element assembly process.

Parameters

[in] sam Auxiliary data describing the FE model topology, etc.

Must be called once before the element assembly loop. The PETSc data structures are initialized and the all symbolic operations that are needed before the actual assembly can start are performed.

Implements SystemMatrix.

References adm, assembled, ProcessAdm::dd, DomainDecomposition::getBlockEqs(), DomainDecomposition::getElms(), DomainDecomposition::getGlobalEq(), PETScSolParams::getLinSysType(), DomainDecomposition::getMaxEq(), DomainDecomposition::getMinEq(), DomainDecomposition::getNoBlocks(), PETScSolParams::getNoBlocks(), DomainDecomposition::isPartitioned(), isvec, matvec, ncol, SAM::nel, nrow, pA, setupBlockSparsity(), setupSparsity(), solParams, LinAlg::SPD, and LinAlg::SYMMETRIC.

◆ preAssemble()

void PETScMatrix::preAssemble	(	const std::vector< IntVec > &	MMNPC,
		size_t	nel
	)

overridevirtual

Initializes the equation sparsity pattern based on element connections.

Parameters

[in]	MMNPC	Matrix of matrices of nodal point correspondances
[in]	nel	Number of elements

Reimplemented from SystemMatrix.

References endAssembly(), m_dd, nrow, pA, and preAllocator().

◆ setParameters()

bool PETScMatrix::setParameters ( bool setup )

Set the linear solver parameters (solver type, preconditioner, tolerances).

Parameters

[in] setup True to setup KSP/PC

Returns: True on success

References adm, ProcessAdm::dd, forcedKSPType, PETScSolParams::getBlock(), DomainDecomposition::getBlockEqs(), PETScSolParams::getDoubleValue(), PETScSolParams::getIntValue(), SettingMap::getStringValue(), PETScSolParams::getStringValue(), isvec, ksp, matvec, PETScSolParams::setupPC(), and solParams.

Referenced by solve(), and solveEig().

◆ setupSparsity()

void PETScMatrix::setupSparsity	(	const IntVec &	elms,
		const SAM &	sam
	)

protected

Setup sparsity pattern for model.

Parameters

[in]	elms	Elements on this process
[in]	sam	Auxiliary data describing the FE model topology, etc.

References adm, ProcessAdm::dd, endAssembly(), DomainDecomposition::getMaxEq(), DomainDecomposition::getMinEq(), pA, and preAllocator().

Referenced by initAssembly().

◆ solve() [1/2]

bool PETScMatrix::solve	(	const SystemVector &	B,
		SystemVector &	x
	)

overridevirtual

Solves the linear system of equations for a given right-hand-side.

Parameters

[in]	B	Right-hand-side vector
[out]	x	Solution vector

Reimplemented from SystemMatrix.

References PETScVector::getVector(), and solve().

◆ solve() [2/2]

bool PETScMatrix::solve	(	SystemVector &	B,
		Real *
	)

overridevirtual

Solves the linear system of equations for a given right-hand-side.

Parameters

B	Right-hand-side vector on input, solution vector on output

Implements SystemMatrix.

References PETScSolParams::getStringValue(), PETScVector::getVector(), and solParams.

Referenced by solve(), and solveMultipleRhs().

◆ solveEig()

bool PETScMatrix::solveEig	(	PETScMatrix &	B,
		RealArray &	eigVal,
		Matrix &	eigVec,
		int	nev,
		Real	shift = `Real(0)`,
		int	iop = `1`
	)

Solves a generalized symmetric-definite eigenproblem.

The eigenproblem is assumed to be on the form A x = λ B x where A ( = *this ) and B both are assumed to be symmetric and B also to be positive definite. The eigenproblem is solved by the SLEPc library subroutine EPSSolve.

See also: SLEPc library documentation.

Parameters

	B	Symmetric and positive definite mass matrix.
[out]	eigVal	Computed eigenvalues
[out]	eigVec	Computed eigenvectors stored column by column
[in]	nev	The number of eigenvalues and eigenvectors to compute
[in]	shift	Eigenvalue shift
[in]	iop	Option telling whether to factorize matrix A or B.

References adm, ProcessAdm::dd, utl::matrix< T >::fillColumn(), DomainDecomposition::getG2LEQ(), PETScSolParams::getIntValue(), DomainDecomposition::isPartitioned(), ksp, pA, utl::matrix< T >::resize(), setParameters(), and solParams.

Referenced by eig::solve().

◆ solveMultipleRhs()

bool PETScMatrix::solveMultipleRhs	(	PETScVectors &	B,
		Matrix &	sField
	)

Solve for multiple right-hand-side vectors.

Parameters

B	Vectors with right-hand-sides to solve for
sField	Resulting vectors stored as a matrix

References PETScVectors::dim(), PETScVectors::get(), m_dd, PETScVectors::size(), and solve().

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

src/LinAlg/PETScMatrix.h
src/LinAlg/PETScMatrix.C

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Member Function Documentation

◆ assemble() [1/4]

◆ assemble() [2/4]

◆ assemble() [3/4]

◆ assemble() [4/4]

◆ dim()

◆ init()

◆ initAssembly()

◆ preAssemble()

◆ setParameters()

◆ setupSparsity()

◆ solve() [1/2]

◆ solve() [2/2]

◆ solveEig()

◆ solveMultipleRhs()