#include <PetscMatTools.hpp>

Collaboration diagram for PetscMatTools:

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)

static void	TurnOffVariableAllocationError (Mat matrix)

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

◆ AddMultipleValues()

template<size_t MATRIX_SIZE>

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

inlinestatic

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 237 of file PetscMatTools.hpp.

References GetOwnershipRange().

Referenced by LinearSystem::AddLhsMultipleValues().

◆ AddToElement()

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().

◆ CheckEquality()

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

static

Returns: true if two matrices are equal to within a given tolerance.

Parameters

mat1	the first matrix
mat2	the second matrix
tol	the tolerance

Definition at line 378 of file PetscMatTools.cpp.

References PetscTools::Destroy().

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

◆ CheckSymmetry()

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

static

Returns: true if the matrix is symmetric Check whether a matrix is symmetric, 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 401 of file PetscMatTools.cpp.

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

◆ Display()

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().

◆ Finalise()

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.

◆ GetElement()

double PetscMatTools::GetElement	(	Mat	matrix,
		PetscInt	row,
		PetscInt	col
	)

static

Returns: 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 310 of file PetscMatTools.cpp.

References GetOwnershipRange().

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

◆ GetMatrixRowDistributed()

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 337 of file PetscMatTools.cpp.

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

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

◆ GetOwnershipRange()

void PetscMatTools::GetOwnershipRange	(	Mat	matrix,
		PetscInt &	lo,
		PetscInt &	hi
	)

static

Returns this process's ownership range of the contents of the matrix via arguments.

Parameters

matrix	the matrix
lo	lowest index owned by this process (returned)
hi	highest index owned by this process (returned)

Definition at line 305 of file PetscMatTools.cpp.

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

◆ GetSize()

unsigned PetscMatTools::GetSize ( Mat matrix )

static

Returns: the size of a matrix

Parameters

matrix the matrix

Definition at line 296 of file PetscMatTools.cpp.

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

◆ SetElement()

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(), MonodomainPurkinjeSolver< ELEMENT_DIM, SPACE_DIM >::SetIdentityBlockToLhsMatrix(), LinearSystem::SetMatrixElement(), and SetRow().

◆ SetOption()

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 328 of file PetscMatTools.cpp.

Referenced by LinearSystem::SetMatrixIsSymmetric().

◆ SetRow()

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 93 of file PetscMatTools.cpp.

References GetOwnershipRange(), and SetElement().

Referenced by LinearSystem::SetMatrixRow().

◆ SwitchWriteMode()

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(), MonodomainPurkinjeSolver< ELEMENT_DIM, SPACE_DIM >::SetIdentityBlockToLhsMatrix(), and LinearSystem::SwitchWriteModeLhsMatrix().

◆ TurnOffVariableAllocationError()

void PetscMatTools::TurnOffVariableAllocationError ( Mat matrix )

static

Tells PETSc to set MAT_NEW_NONZERO_ALLOCATION_ERR to false.

This should be called immediately after PetscTools::SetupMat and before any other operations on the matrix.

** Currently only used in PETSc 3.3 and later ** in PETSc 3.2 and earlier MAT_NEW_NONZERO_ALLOCATION_ERR defaults to false in PETSc 3.3 MAT_NEW_NONZERO_ALLOCATION_ERR defaults to true

Parameters

matrix The matrix to set

Definition at line 414 of file PetscMatTools.cpp.

Referenced by AbstractBidomainSolver< DIM, DIM >::InitialiseForSolve(), and AbstractExtendedBidomainSolver< ELEMENT_DIM, SPACE_DIM >::InitialiseForSolve().

◆ Zero()

void PetscMatTools::Zero ( Mat matrix )

static

Zero all entries of a matrix.

Parameters

matrix the matrix

Definition at line 291 of file PetscMatTools.cpp.

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

◆ ZeroColumn()

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 255 of file PetscMatTools.cpp.

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

Referenced by LinearSystem::ZeroMatrixColumn().

◆ ZeroRowsAndColumnsWithValueOnDiagonal()

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 191 of file PetscMatTools.cpp.

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

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

◆ ZeroRowsWithValueOnDiagonal()

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 109 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

◆ AddMultipleValues()

◆ AddToElement()

◆ CheckEquality()

◆ CheckSymmetry()

◆ Display()

◆ Finalise()

◆ GetElement()

◆ GetMatrixRowDistributed()

◆ GetOwnershipRange()

◆ GetSize()

◆ SetElement()

◆ SetOption()

◆ SetRow()

◆ SwitchWriteMode()

◆ TurnOffVariableAllocationError()

◆ Zero()

◆ ZeroColumn()

◆ ZeroRowsAndColumnsWithValueOnDiagonal()

◆ ZeroRowsWithValueOnDiagonal()