#include <PetscMatTools.hpp>

Static Public Member Functions
static void	SetElement (Mat matrix, PetscInt row, PetscInt col, double value)
static void	AddToElement (Mat matrix, PetscInt row, PetscInt col, double value)
static void	Finalise (Mat matrix)
static void	SwitchWriteMode (Mat matrix)
static void	Display (Mat matrix)
static void	SetRow (Mat matrix, PetscInt row, double value)
static void	ZeroRowsWithValueOnDiagonal (Mat matrix, std::vector< unsigned > &rRows, double diagonalValue)
static void	ZeroRowsAndColumnsWithValueOnDiagonal (Mat matrix, std::vector< unsigned > rowColIndices, double diagonalValue)
static void	ZeroColumn (Mat matrix, PetscInt col)
static void	Zero (Mat matrix)
static unsigned	GetSize (Mat matrix)
static void	GetOwnershipRange (Mat matrix, PetscInt &lo, PetscInt &hi)
static double	GetElement (Mat matrix, PetscInt row, PetscInt col)
static void	SetOption (Mat matrix, MatOption option)
static Vec	GetMatrixRowDistributed (Mat matrix, unsigned rowIndex)
static bool	CheckEquality (const Mat mat1, const Mat mat2, double tol=1e-10)
static bool	CheckSymmetry (const Mat matrix, double tol=1e-10)
template<size_t MATRIX_SIZE>
static void	AddMultipleValues (Mat matrix, unsigned *matrixRowAndColIndices, c_matrix< double, MATRIX_SIZE, MATRIX_SIZE > &rSmallMatrix)

Detailed Description

A collection of static methods for working with PETSc matrices.

Definition at line 48 of file PetscMatTools.hpp.

Member Function Documentation

template<size_t MATRIX_SIZE>

static void PetscMatTools::AddMultipleValues	(	Mat	matrix,
		unsigned *	matrixRowAndColIndices,
		c_matrix< double, MATRIX_SIZE, MATRIX_SIZE > &	rSmallMatrix
	)		`[inline, static]`

Add multiple values to a matrix.

Parameters:

matrix	the matrix
matrixRowAndColIndices	mapping from index of the ublas matrix (see param below) to index of the PETSc matrix of this linear system
rSmallMatrix	Ublas matrix containing the values to be added

N.B. Values which are not local (ie the row is not owned) will be skipped.

Definition at line 222 of file PetscMatTools.hpp.

References GetOwnershipRange().

Referenced by LinearSystem::AddLhsMultipleValues().

void PetscMatTools::AddToElement	(	Mat	matrix,
		PetscInt	row,
		PetscInt	col,
		double	value
	)		`[static]`

Add the specified value to an entry of a matrix.

Parameters:

matrix	the matrix
row	the row index
col	the column index
value	the value for this entry

Definition at line 56 of file PetscMatTools.cpp.

References GetOwnershipRange().

Referenced by LinearSystem::AddToMatrixElement(), and NodeBasedCellPopulationWithBuskeUpdate< DIM >::UpdateNodeLocations().

bool PetscMatTools::CheckEquality	(	const Mat	mat1,
		const Mat	mat2,
		double	tol = `1e-10`
	)		`[static]`

Check whether two matrices are equal to within a given tolerance.

Parameters:

mat1	the first matrix
mat2	the second matrix
tol	the tolerance

Definition at line 369 of file PetscMatTools.cpp.

References PetscTools::Destroy().

Referenced by CheckSymmetry(), and AbstractNonlinearAssemblerSolverHybrid< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::VerifyJacobian().

bool PetscMatTools::CheckSymmetry	(	const Mat	matrix,
		double	tol = `1e-10`
	)		`[static]`

Check whether a matrix is symmetrix, to within a given tolerance, by checking if it is (approximately) equal to its transpose.

Note that while there is a PETSc method MatIsSymmetric, it won't work in parallel on some PETSc versions: "Matrix of type <mpiaij> does not support checking for symmetric!"

Also checking for exact equality of the transpose can break on 32bit systems.

Parameters:

matrix	the matrix to check
tol	the tolerance

Definition at line 392 of file PetscMatTools.cpp.

References CheckEquality(), and PetscTools::Destroy().

void PetscMatTools::Display ( Mat matrix ) [static]

Display a matrix.

Parameters:

matrix the matrix

Definition at line 79 of file PetscMatTools.cpp.

Referenced by LinearSystem::DisplayMatrix().

void PetscMatTools::Finalise ( Mat matrix ) [static]

Sets up the matrix ready for use, e.g. in solving a linear system. This is a wrapper to PETSc functions like MatAssemblyBegin(matrix, MAT_FINAL_ASSEMBLY).

Parameters:

matrix the matrix

Definition at line 67 of file PetscMatTools.cpp.

Referenced by AbstractContinuumMechanicsSolver< DIM >::ApplyDirichletBoundaryConditions(), BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::ApplyDirichletToNonlinearJacobian(), StokesFlowSolver< DIM >::AssembleSystem(), AbstractNonlinearAssemblerSolverHybrid< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::ComputeJacobian(), AbstractNonlinearAssemblerSolverHybrid< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::ComputeJacobianNumerically(), LinearSystem::FinaliseLhsMatrix(), LinearSystem::FinalisePrecondMatrix(), AbstractNonlinearElasticitySolver< DIM >::FinishAssembleSystem(), NodePartitioner< ELEMENT_DIM, SPACE_DIM >::PetscMatrixPartitioning(), OperatorSplittingMonodomainSolver< ELEMENT_DIM, SPACE_DIM >::SetupLinearSystem(), MonodomainSolver< ELEMENT_DIM, SPACE_DIM >::SetupLinearSystem(), ExtendedBidomainSolver< ELEM_DIM, SPACE_DIM >::SetupLinearSystem(), BidomainSolver< ELEMENT_DIM, SPACE_DIM >::SetupLinearSystem(), NodeBasedCellPopulationWithBuskeUpdate< DIM >::UpdateNodeLocations(), ZeroColumn(), ZeroRowsAndColumnsWithValueOnDiagonal(), and ZeroRowsWithValueOnDiagonal().

double PetscMatTools::GetElement	(	Mat	matrix,
		PetscInt	row,
		PetscInt	col
	)		`[static]`

Return an element of a matrix. May only be called for elements you own.

Parameters:

matrix	the matrix
row	the row index
col	the column index

Definition at line 301 of file PetscMatTools.cpp.

References GetOwnershipRange().

Referenced by LinearSystem::GetMatrixElement(), and ZeroColumn().

Vec PetscMatTools::GetMatrixRowDistributed	(	Mat	matrix,
		unsigned	rowIndex
	)		`[static]`

Returns the i-th row of the LHS matrix as a distributed PETSc Vec

Parameters:

matrix	the matrix
rowIndex	the row index

Returns:: rowIndex-th row of the matrix in distributed format

Definition at line 328 of file PetscMatTools.cpp.

References PetscTools::CreateVec(), GetOwnershipRange(), and GetSize().

Referenced by AbstractContinuumMechanicsSolver< DIM >::ApplyDirichletBoundaryConditions().

void PetscMatTools::GetOwnershipRange	(	Mat	matrix,
		PetscInt &	lo,
		PetscInt &	hi
	)		`[static]`

Get this process's ownership range of the contents of the system.

Parameters:

matrix	the matrix
lo	lowest index owned by this process
hi	highest index owned by this process

Definition at line 296 of file PetscMatTools.cpp.

Referenced by AddMultipleValues(), AddToElement(), GetElement(), GetMatrixRowDistributed(), SetElement(), SetRow(), ZeroColumn(), and ZeroRowsAndColumnsWithValueOnDiagonal().

unsigned PetscMatTools::GetSize ( Mat matrix ) [static]

Get the size of a matrix

Parameters:

matrix the matrix

Definition at line 287 of file PetscMatTools.cpp.

Referenced by AbstractContinuumMechanicsAssembler< DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX >::DoAssemble(), and GetMatrixRowDistributed().

void PetscMatTools::SetElement	(	Mat	matrix,
		PetscInt	row,
		PetscInt	col,
		double	value
	)		`[static]`

Change one of the entries of a matrix to the specified value.

Parameters:

matrix	the matrix
row	the row index
col	the column index
value	the value for this entry

Definition at line 45 of file PetscMatTools.cpp.

References GetOwnershipRange().

Referenced by AbstractContinuumMechanicsSolver< DIM >::AddIdentityBlockForDummyPressureVariables(), BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::ApplyPeriodicBcsToLinearProblem(), AbstractNonlinearAssemblerSolverHybrid< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::ComputeJacobianNumerically(), AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >::FinaliseForBath(), LinearSystem::SetMatrixElement(), and SetRow().

void PetscMatTools::SetOption	(	Mat	matrix,
		MatOption	option
	)		`[static]`

Set a PETSc matrix option to be true, using the PETSc method MatSetOption.

Parameters:

matrix	the matrix for which to set the option
option	the option to set

Definition at line 319 of file PetscMatTools.cpp.

Referenced by LinearSystem::SetMatrixIsSymmetric().

void PetscMatTools::SetRow	(	Mat	matrix,
		PetscInt	row,
		double	value
	)		`[static]`

Set all entries in a given row of a matrix to a certain value. This must be called by the process who owns the row, (but other processors will treat it as a null-op

Parameters:

matrix	the matrix
row	the row index
value	the value to set each entry in this row

Definition at line 84 of file PetscMatTools.cpp.

References GetOwnershipRange(), and SetElement().

Referenced by LinearSystem::SetMatrixRow().

void PetscMatTools::SwitchWriteMode ( Mat matrix ) [static]

This must be called if switching between inserting or adding values to the matrix, to ensure all processes are in sync. This is a wrapper to PETSc functions like MatAssemblyBegin(matrix, MAT_FLUSH_ASSEMBLY).

Parameters:

matrix the matrix

Definition at line 73 of file PetscMatTools.cpp.

Referenced by StokesFlowSolver< DIM >::AssembleSystem(), IncompressibleNonlinearElasticitySolver< DIM >::AssembleSystem(), AbstractNonlinearAssemblerSolverHybrid< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::ComputeJacobian(), AbstractNonlinearElasticitySolver< DIM >::FinishAssembleSystem(), and LinearSystem::SwitchWriteModeLhsMatrix().

void PetscMatTools::Zero ( Mat matrix ) [static]

Zero all entries of a matrix.

Parameters:

matrix the matrix

Definition at line 282 of file PetscMatTools.cpp.

Referenced by IncompressibleNonlinearElasticitySolver< DIM >::AssembleSystem(), CompressibleNonlinearElasticitySolver< DIM >::AssembleSystem(), AbstractFeVolumeIntegralAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX, INTERPOLATION_LEVEL >::DoAssemble(), AbstractFeCableIntegralAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX, INTERPOLATION_LEVEL >::DoAssemble(), AbstractContinuumMechanicsAssembler< DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX >::DoAssemble(), and LinearSystem::ZeroLhsMatrix().

void PetscMatTools::ZeroColumn	(	Mat	matrix,
		PetscInt	col
	)		`[static]`

Zero a column of a matrix.

Unfortunately there is no equivalent method in Petsc, so this has to be done carefully to ensure that the sparsity structure of the matrix is not broken. Only owned entries which are non-zero are zeroed.

Parameters:

matrix	the matrix
col	the column index

Definition at line 246 of file PetscMatTools.cpp.

References Finalise(), GetElement(), and GetOwnershipRange().

Referenced by LinearSystem::ZeroMatrixColumn().

void PetscMatTools::ZeroRowsAndColumnsWithValueOnDiagonal	(	Mat	matrix,
		std::vector< unsigned >	rowColIndices,
		double	diagonalValue
	)		`[static]`

Zero several rows and columns of a matrix, putting a given value on the diagonal.

Parameters:

matrix	the matrix
rowColIndices	A list of indices. All the rows with these indices, and all the columns with these indices, will be zeroed. This vector is copied (ie not passed in by reference), as it will be sorted into ascending order
diagonalValue	value to put in the diagonal entries (of the zeroed rows)

Definition at line 182 of file PetscMatTools.cpp.

References Finalise(), GetOwnershipRange(), and ZeroRowsWithValueOnDiagonal().

Referenced by AbstractContinuumMechanicsSolver< DIM >::ApplyDirichletBoundaryConditions(), and LinearSystem::ZeroMatrixRowsAndColumnsWithValueOnDiagonal().

void PetscMatTools::ZeroRowsWithValueOnDiagonal	(	Mat	matrix,
		std::vector< unsigned > &	rRows,
		double	diagonalValue
	)		`[static]`

Zero several rows of a matrix, putting a given value in the diagonal entries.

*Massively* less expensive than zeroing each matrix row individually

Parameters:

matrix	the matrix
rRows	std::vector of rows to be zeroed
diagonalValue	value to put in the diagonal entries (of the zeroed rows)

Definition at line 100 of file PetscMatTools.cpp.

References Finalise(), and PETSC_DESTROY_PARAM.

Referenced by AbstractContinuumMechanicsSolver< DIM >::ApplyDirichletBoundaryConditions(), BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::ApplyDirichletToNonlinearJacobian(), LinearSystem::ZeroMatrixRowsWithValueOnDiagonal(), and ZeroRowsAndColumnsWithValueOnDiagonal().

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

linalg/src/PetscMatTools.hpp
linalg/src/PetscMatTools.cpp

Static Public Member Functions

Detailed Description

Member Function Documentation