PetscMatTools Class Reference

#include <PetscMatTools.hpp>

List of all members.

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 > &rRowColIndices, 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 41 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 214 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 47 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 359 of file PetscMatTools.cpp.

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 382 of file PetscMatTools.cpp.

References CheckEquality().

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

Display a matrix.

Parameters:
matrix the matrix

Definition at line 70 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 58 of file PetscMatTools.cpp.

Referenced by AbstractNonlinearElasticitySolver< DIM >::ApplyDirichletBoundaryConditions(), BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::ApplyDirichletToNonlinearJacobian(), AbstractNonlinearAssemblerSolverHybrid< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::ComputeJacobian(), AbstractNonlinearAssemblerSolverHybrid< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::ComputeJacobianNumerically(), LinearSystem::FinaliseLhsMatrix(), LinearSystem::FinalisePrecondMatrix(), AbstractNonlinearElasticitySolver< DIM >::FinishAssembleSystem(), 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 291 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 318 of file PetscMatTools.cpp.

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

Referenced by AbstractNonlinearElasticitySolver< 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 286 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 277 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 36 of file PetscMatTools.cpp.

References GetOwnershipRange().

Referenced by 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 309 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 75 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 64 of file PetscMatTools.cpp.

Referenced by 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 272 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 236 of file PetscMatTools.cpp.

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

Referenced by LinearSystem::ZeroMatrixColumn().

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

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

Parameters:
matrix the matrix
rRowColIndices A list of indices. All the rows with these indices, and all the columns with these indices, will be zeroed.
diagonalValue value to put in the diagonal entries (of the zeroed rows)

Definition at line 169 of file PetscMatTools.cpp.

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

Referenced by AbstractNonlinearElasticitySolver< 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 91 of file PetscMatTools.cpp.

References Finalise().

Referenced by AbstractNonlinearElasticitySolver< 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:
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