LinearSystem Class Reference

#include <LinearSystem.hpp>

Collaboration diagram for LinearSystem:

List of all members.

Public Member Functions

LinearSystem (PetscInt lhsVectorSize, unsigned rowPreallocation=UINT_MAX)

LinearSystem (Vec templateVector, unsigned rowPreallocation)

LinearSystem (Vec residualVector, Mat jacobianMatrix)

LinearSystem (PetscInt lhsVectorSize, Mat lhsMatrix, Vec rhsVector)

~LinearSystem ()

void SetMatrixElement (PetscInt row, PetscInt col, double value)

void AddToMatrixElement (PetscInt row, PetscInt col, double value)

void AssembleFinalLinearSystem ()

void AssembleIntermediateLinearSystem ()

void AssembleFinalLhsMatrix ()

void AssembleFinalPrecondMatrix ()

void AssembleIntermediateLhsMatrix ()

void AssembleRhsVector ()

void SetMatrixIsSymmetric (bool isSymmetric=true)

bool IsMatrixSymmetric ()

void SetMatrixIsConstant (bool matrixIsConstant)

void SetRelativeTolerance (double relativeTolerance)

void SetAbsoluteTolerance (double absoluteTolerance)

void SetKspType (const char *kspType)

void SetPcType (const char *pcType, boost::shared_ptr< std::vector< PetscInt > > pBathNodes=boost::shared_ptr< std::vector< PetscInt > >())

void DisplayMatrix ()

void DisplayRhs ()

void SetMatrixRow (PetscInt row, double value)

Vec GetMatrixRowDistributed (unsigned rowIndex)

void ZeroMatrixRowsWithValueOnDiagonal (std::vector< unsigned > &rRows, double diagonalValue)

void ZeroMatrixRowsAndColumnsWithValueOnDiagonal (std::vector< unsigned > &rRowColIndices, double diagonalValue)

void ZeroMatrixColumn (PetscInt col)

void ZeroLhsMatrix ()

void ZeroRhsVector ()

void ZeroLinearSystem ()

Vec Solve (Vec lhsGuess=NULL)

void SetRhsVectorElement (PetscInt row, double value)

void AddToRhsVectorElement (PetscInt row, double value)

unsigned GetSize () const

void SetNullBasis (Vec nullbasis[], unsigned numberOfBases)

void RemoveNullSpace ()

Vec & rGetRhsVector ()

Vec GetRhsVector () const

Mat & rGetLhsMatrix ()

Mat GetLhsMatrix () const

Mat & rGetPrecondMatrix ()

Vec & rGetDirichletBoundaryConditionsVector ()

void GetOwnershipRange (PetscInt &lo, PetscInt &hi)

double GetMatrixElement (PetscInt row, PetscInt col)

double GetRhsVectorElement (PetscInt row)

unsigned GetNumIterations () const

template<size_t MATRIX_SIZE>

void AddLhsMultipleValues (unsigned *matrixRowAndColIndices, c_matrix< double, MATRIX_SIZE, MATRIX_SIZE > &rSmallMatrix)

template<size_t VECTOR_SIZE>

void AddRhsMultipleValues (unsigned *vectorIndices, c_vector< double, VECTOR_SIZE > &smallVector)

void SetPrecondMatrixIsDifferentFromLhs (bool precondIsDifferent=true)

void SetUseFixedNumberIterations (bool useFixedNumberIterations=true, unsigned evaluateNumItsEveryNSolves=UINT_MAX)

void ResetKspSolver ()

Private Member Functions

template<class Archive>

void serialize (Archive &archive, const unsigned int version)

Private Attributes

Mat mLhsMatrix

Mat mPrecondMatrix

Vec mRhsVector

PetscInt mSize

PetscInt mOwnershipRangeLo

PetscInt mOwnershipRangeHi

MatNullSpace mMatNullSpace

bool mDestroyMatAndVec

KSP mKspSolver

bool mKspIsSetup

double mNonZerosUsed

bool mMatrixIsConstant

double mTolerance

bool mUseAbsoluteTolerance

std::string mKspType

std::string mPcType

Vec mDirichletBoundaryConditionsVector

PCBlockDiagonal * mpBlockDiagonalPC

PCLDUFactorisation * mpLDUFactorisationPC

PCTwoLevelsBlockDiagonal * mpTwoLevelsBlockDiagonalPC

boost::shared_ptr< std::vector
< PetscInt > > mpBathNodes

bool mPrecondMatrixIsNotLhs

unsigned mRowPreallocation

bool mUseFixedNumberIterations

unsigned mEvaluateNumItsEveryNSolves

void * mpConvergenceTestContext

unsigned mNumSolves

PetscReal mEigMin

PetscReal mEigMax

bool mForceSpectrumReevaluation

Friends

class TestLinearSystem

class TestPCBlockDiagonal

class TestPCTwoLevelsBlockDiagonal

class TestPCLDUFactorisation

class TestChebyshevIteration

class boost::serialization::access

Detailed Description

Linear System class. Stores and solves a linear equation of the form Ax=b, where A is a square matrix and x and b are column vectors. The class uses PETSc.

Definition at line 59 of file LinearSystem.hpp.

Constructor & Destructor Documentation

LinearSystem::LinearSystem	(	PetscInt	lhsVectorSize,
		unsigned	rowPreallocation = `UINT_MAX`
	)

Constructor.

Parameters:

	lhsVectorSize	the size of the LHS vector
	rowPreallocation	the max number of nonzero entries expected on a row a value of 0 is allowed: no preallocation is then done and the user must preallocate the memory for the matrix themselves. the default value allows for small size systems to be set as dense matrices automatically.

Todo:: : if we create a linear system object outside a cardiac solver, these are gonna be the default solver and preconditioner. Not consitent with ChasteDefaults.xml though...

Definition at line 45 of file LinearSystem.cpp.

References PetscTools::CreateVec(), EXCEPTION, mKspType, mLhsMatrix, mNumSolves, mOwnershipRangeHi, mOwnershipRangeLo, mPcType, mRhsVector, mRowPreallocation, mSize, and PetscTools::SetupMat().

LinearSystem::LinearSystem	(	Vec	templateVector,
		unsigned	rowPreallocation
	)

Alternative constructor.

Create a linear system, where the size is based on the size of a given PETSc vec.

The LHS & RHS vectors will be created by duplicating this vector's settings. This should avoid problems with using VecScatter on bidomain simulation results.

Parameters:

	templateVector	a PETSc vec
	rowPreallocation	the max number of nonzero entries expected on a row

Todo:: : if we create a linear system object outside a cardiac solver, these are gonna be the default solver and preconditioner. Not consitent with ChasteDefaults.xml though...

Definition at line 137 of file LinearSystem.cpp.

References mKspType, mLhsMatrix, mNumSolves, mOwnershipRangeHi, mOwnershipRangeLo, mPcType, mRhsVector, mRowPreallocation, mSize, and PetscTools::SetupMat().

LinearSystem::LinearSystem	(	Vec	residualVector,
		Mat	jacobianMatrix
	)

Alternative constructor.

Create a linear system which wraps the provided PETSc objects so we can access them using our API. Either of the objects may be NULL, but at least one of them must not be.

Useful for storing residuals and jacobians when solving nonlinear PDEs.

Parameters:

	residualVector	the residual vector
	jacobianMatrix	the Jacobian matrix

Todo:: : if we create a linear system object outside a cardiac solver, these are gonna be the default solver and preconditioner. Not consitent with ChasteDefaults.xml though...

Definition at line 178 of file LinearSystem.cpp.

References mKspType, mLhsMatrix, mNumSolves, mOwnershipRangeHi, mOwnershipRangeLo, mPcType, mRhsVector, mRowPreallocation, and mSize.

LinearSystem::LinearSystem	(	PetscInt	lhsVectorSize,
		Mat	lhsMatrix,
		Vec	rhsVector
	)

Alternative constructor for archiving.

Parameters:

	lhsVectorSize	the size of the LHS vector
	lhsMatrix	the RHS matrix
	rhsVector	the RHS vector

Definition at line 100 of file LinearSystem.cpp.

References mLhsMatrix, mNumSolves, mOwnershipRangeHi, mOwnershipRangeLo, and mRhsVector.

LinearSystem::~LinearSystem ( )

Destructor.

Todo:: Never tested in linalg component

Definition at line 242 of file LinearSystem.cpp.

References PetscTools::AmMaster(), mDestroyMatAndVec, mDirichletBoundaryConditionsVector, mKspIsSetup, mKspSolver, mLhsMatrix, mMatNullSpace, mNumSolves, mpBlockDiagonalPC, mpConvergenceTestContext, mpLDUFactorisationPC, mPrecondMatrix, mPrecondMatrixIsNotLhs, mpTwoLevelsBlockDiagonalPC, and mRhsVector.

Member Function Documentation

template<class Archive>

void LinearSystem::serialize	(	Archive &	archive,
		const unsigned int	version
	)			`[inline, private]`

Archive the member variables.

Parameters:

	archive
	version

Definition at line 156 of file LinearSystem.hpp.

References mKspType, mMatrixIsConstant, mNonZerosUsed, mPcType, mTolerance, and mUseAbsoluteTolerance.

void LinearSystem::SetMatrixElement	(	PetscInt	row,
		PetscInt	col,
		double	value
	)

Change one of the entires of the matrix to the specified value.

Parameters:

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

Definition at line 299 of file LinearSystem.cpp.

References mLhsMatrix, and PetscMatTools::SetElement().

Referenced by AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >::FinaliseLinearSystem().

void LinearSystem::AddToMatrixElement	(	PetscInt	row,
		PetscInt	col,
		double	value
	)

Add the specified value to an entry of the matrix.

Parameters:

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

Definition at line 304 of file LinearSystem.cpp.

References PetscMatTools::AddToElement(), and mLhsMatrix.

void LinearSystem::AssembleFinalLinearSystem ( )

Call this before Solve().

This calls AssembleFinalLhsMatrix() and AssembleRhsVector().

Definition at line 309 of file LinearSystem.cpp.

References AssembleFinalLhsMatrix(), and AssembleRhsVector().

Referenced by BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::ApplyDirichletToLinearProblem().

void LinearSystem::AssembleIntermediateLinearSystem ( )

Should be called before AddToMatrixElement.

This calls AssembleIntermediateLhsMatrix() and AssembleRhsVector().

Definition at line 315 of file LinearSystem.cpp.

References AssembleIntermediateLhsMatrix(), and AssembleRhsVector().

void LinearSystem::AssembleFinalLhsMatrix ( )

Sets up the PETSc matrix left-hand-side mLhsMatrix

Definition at line 321 of file LinearSystem.cpp.

References PetscMatTools::AssembleFinal(), and mLhsMatrix.

Referenced by AssembleFinalLinearSystem(), AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >::FinaliseLinearSystem(), AbstractAssemblerSolverHybrid< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, INTERPOLATION_LEVEL >::SetupGivenLinearSystem(), OperatorSplittingMonodomainSolver< ELEMENT_DIM, SPACE_DIM >::SetupLinearSystem(), MatrixBasedMonodomainSolver< ELEMENT_DIM, SPACE_DIM >::SetupLinearSystem(), MatrixBasedBidomainSolver< ELEMENT_DIM, SPACE_DIM >::SetupLinearSystem(), BasicMonodomainSolver< ELEMENT_DIM, SPACE_DIM >::SetupLinearSystem(), and BasicBidomainSolver< ELEMENT_DIM, SPACE_DIM >::SetupLinearSystem().

void LinearSystem::AssembleFinalPrecondMatrix ( )

Sets up the PETSc matrix used for preconditioning.

Definition at line 331 of file LinearSystem.cpp.

References PetscMatTools::AssembleFinal(), and mPrecondMatrix.

Referenced by MatrixBasedMonodomainSolver< ELEMENT_DIM, SPACE_DIM >::SetupLinearSystem().

void LinearSystem::AssembleIntermediateLhsMatrix ( )

Sets up the PETSc matrix left-hand-side mLhsMatrix

Definition at line 326 of file LinearSystem.cpp.

References PetscMatTools::AssembleIntermediate(), and mLhsMatrix.

Referenced by AssembleIntermediateLinearSystem(), AbstractAssemblerSolverHybrid< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, INTERPOLATION_LEVEL >::SetupGivenLinearSystem(), and MatrixBasedBidomainSolver< ELEMENT_DIM, SPACE_DIM >::SetupLinearSystem().

void LinearSystem::AssembleRhsVector ( )

Sets up the PETSc vector right-hand-side mRhsVector

Definition at line 336 of file LinearSystem.cpp.

References PetscVecTools::Assemble(), and mRhsVector.

Referenced by AssembleFinalLinearSystem(), AssembleIntermediateLinearSystem(), AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >::FinaliseLinearSystem(), AbstractAssemblerSolverHybrid< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, INTERPOLATION_LEVEL >::SetupGivenLinearSystem(), OperatorSplittingMonodomainSolver< ELEMENT_DIM, SPACE_DIM >::SetupLinearSystem(), MatrixBasedMonodomainSolver< ELEMENT_DIM, SPACE_DIM >::SetupLinearSystem(), MatrixBasedBidomainSolver< ELEMENT_DIM, SPACE_DIM >::SetupLinearSystem(), BasicMonodomainSolver< ELEMENT_DIM, SPACE_DIM >::SetupLinearSystem(), and BasicBidomainSolver< ELEMENT_DIM, SPACE_DIM >::SetupLinearSystem().

void LinearSystem::SetMatrixIsSymmetric ( bool isSymmetric = true )

Force PETSc to treat the matrix in this linear system as symmetric from now on.

Parameters:

isSymmetric

whether the matrix is symmetric or not (defaults to true)

Todo:: : shall we allow modifying the symmetry flag anytime?

Definition at line 526 of file LinearSystem.cpp.

References mLhsMatrix, and PetscMatTools::SetOption().

Referenced by SimpleLinearEllipticSolver< ELEMENT_DIM, SPACE_DIM >::InitialiseForSolve(), OperatorSplittingMonodomainSolver< ELEMENT_DIM, SPACE_DIM >::InitialiseForSolve(), AbstractMonodomainSolver< ELEMENT_DIM, SPACE_DIM >::InitialiseForSolve(), AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >::InitialiseForSolve(), and CellBasedSimulationWithPdesAssembler< DIM >::InitialiseForSolve().

bool LinearSystem::IsMatrixSymmetric ( )

Get whether PETSc considers the matrix in this linear system as symmetric or not.

Returns:: whether the matrix is symmetric or not.

Definition at line 550 of file LinearSystem.cpp.

References mLhsMatrix.

Referenced by BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::ApplyDirichletToLinearProblem().

void LinearSystem::SetMatrixIsConstant ( bool matrixIsConstant )

Set mMatrixIsConstant.

Parameters:

matrixIsConstant

whether the matrix is constant

Definition at line 561 of file LinearSystem.cpp.

References mMatrixIsConstant.

void LinearSystem::SetRelativeTolerance ( double relativeTolerance )

Set the relative tolerance.

Parameters:

relativeTolerance

the relative tolerance

Definition at line 566 of file LinearSystem.cpp.

References mKspIsSetup, mKspSolver, mTolerance, and mUseAbsoluteTolerance.

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

void LinearSystem::SetAbsoluteTolerance ( double absoluteTolerance )

Set the absolute tolerance.

Parameters:

absoluteTolerance

the absolute tolerance

Definition at line 576 of file LinearSystem.cpp.

References mKspIsSetup, mKspSolver, mTolerance, and mUseAbsoluteTolerance.

Referenced by OperatorSplittingMonodomainSolver< ELEMENT_DIM, SPACE_DIM >::InitialiseForSolve(), AbstractMonodomainSolver< ELEMENT_DIM, SPACE_DIM >::InitialiseForSolve(), and AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >::InitialiseForSolve().

void LinearSystem::SetKspType ( const char * kspType )

Set the KSP solver type (see PETSc KSPSetType() for valid arguments).

Parameters:

kspType

the KSP solver type

Definition at line 586 of file LinearSystem.cpp.

References mKspIsSetup, mKspSolver, and mKspType.

Referenced by AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >::FinaliseLinearSystem(), SimpleLinearEllipticSolver< ELEMENT_DIM, SPACE_DIM >::InitialiseForSolve(), OperatorSplittingMonodomainSolver< ELEMENT_DIM, SPACE_DIM >::InitialiseForSolve(), AbstractMonodomainSolver< ELEMENT_DIM, SPACE_DIM >::InitialiseForSolve(), and AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >::InitialiseForSolve().

void LinearSystem::SetPcType	(	const char *	pcType,
		boost::shared_ptr< std::vector< PetscInt > >	pBathNodes = `boost::shared_ptr<std::vector<PetscInt> >()`
	)

Set the preconditioner type (see PETSc PCSetType() for valid arguments).

Parameters:

	pcType	the preconditioner type
	pBathNodes	the list of nodes defining the bath

Todo:: : #1082 is this the way of defining a null pointer as the default value of pBathNodes?

Todo:: : #1082 use a single pointer to abstract class

Todo:: : #1082 use a single pointer to abstract class

Todo:: : #1082 use a single pointer to abstract class

Definition at line 596 of file LinearSystem.cpp.

References mKspIsSetup, mKspSolver, mpBathNodes, mpBlockDiagonalPC, mPcType, mpLDUFactorisationPC, mpTwoLevelsBlockDiagonalPC, and TERMINATE.

Referenced by OperatorSplittingMonodomainSolver< ELEMENT_DIM, SPACE_DIM >::InitialiseForSolve(), AbstractMonodomainSolver< ELEMENT_DIM, SPACE_DIM >::InitialiseForSolve(), and AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >::InitialiseForSolve().

void LinearSystem::DisplayMatrix ( )

Display the left-hand side matrix.

Definition at line 351 of file LinearSystem.cpp.

References PetscMatTools::Display(), and mLhsMatrix.

void LinearSystem::DisplayRhs ( )

Display the right-hand side vector.

Definition at line 356 of file LinearSystem.cpp.

References PetscVecTools::Display(), and mRhsVector.

void LinearSystem::SetMatrixRow	(	PetscInt	row,
		double	value
	)

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:

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

Definition at line 361 of file LinearSystem.cpp.

References mLhsMatrix, and PetscMatTools::SetRow().

Vec LinearSystem::GetMatrixRowDistributed ( unsigned rowIndex )

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

Parameters:

rowIndex

the row index

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

Definition at line 366 of file LinearSystem.cpp.

References PetscMatTools::GetMatrixRowDistributed(), and mLhsMatrix.

Referenced by BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::ApplyDirichletToLinearProblem().

void LinearSystem::ZeroMatrixRowsWithValueOnDiagonal	(	std::vector< unsigned > &	rRows,
		double	diagonalValue
	)

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

*Massively* less expensive than zeroing each matrix rowindividually

Parameters:

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

Definition at line 371 of file LinearSystem.cpp.

References mLhsMatrix, and PetscMatTools::ZeroRowsWithValueOnDiagonal().

Referenced by BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::ApplyDirichletToLinearProblem(), and AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >::FinaliseLinearSystem().

void LinearSystem::ZeroMatrixRowsAndColumnsWithValueOnDiagonal	(	std::vector< unsigned > &	rRowColIndices,
		double	diagonalValue
	)

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

Parameters:

	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 377 of file LinearSystem.cpp.

References mLhsMatrix, and PetscMatTools::ZeroRowsAndColumnsWithValueOnDiagonal().

Referenced by BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::ApplyDirichletToLinearProblem().

void LinearSystem::ZeroMatrixColumn ( PetscInt col )

Zero a column of the left-hand side 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:

col

the column index

Definition at line 382 of file LinearSystem.cpp.

References mLhsMatrix, and PetscMatTools::ZeroColumn().

void LinearSystem::ZeroLhsMatrix ( )

Zero all entries of the left-hand side matrix.

Definition at line 392 of file LinearSystem.cpp.

References mLhsMatrix, and PetscMatTools::Zero().

Referenced by ZeroLinearSystem().

void LinearSystem::ZeroRhsVector ( )

Zero all entries of the right-hand side vector.

Definition at line 387 of file LinearSystem.cpp.

References mRhsVector, and PetscVecTools::Zero().

Referenced by ZeroLinearSystem().

void LinearSystem::ZeroLinearSystem ( )

Zero all entries of the left-hand side matrix and right-hand side vector.

Definition at line 397 of file LinearSystem.cpp.

References ZeroLhsMatrix(), and ZeroRhsVector().

Referenced by SimpleNewtonNonlinearSolver::Solve().

Vec LinearSystem::Solve ( Vec lhsGuess = NULL )

Solve the linear system.

Parameters:

lhsGuess

an optional initial guess for the solution (defaults to NULL)

Todo:: never tested in linalg component

Todo:: Should it be compulsory for the caller to supply this and manage the memory?

Todo:: #1695 Store this number in a member variable.

Definition at line 656 of file LinearSystem.cpp.

References PetscTools::AmMaster(), GenericEventHandler< 13, HeartEventHandler >::BeginEvent(), GenericEventHandler< 13, HeartEventHandler >::EndEvent(), EXCEPTION, mEigMax, mEigMin, mEvaluateNumItsEveryNSolves, mForceSpectrumReevaluation, mKspIsSetup, mKspSolver, mKspType, mLhsMatrix, mMatNullSpace, mMatrixIsConstant, mNonZerosUsed, mNumSolves, mpBathNodes, mpBlockDiagonalPC, mpConvergenceTestContext, mPcType, mpLDUFactorisationPC, mPrecondMatrix, mPrecondMatrixIsNotLhs, mpTwoLevelsBlockDiagonalPC, mRhsVector, mSize, mTolerance, mUseAbsoluteTolerance, mUseFixedNumberIterations, Timer::Print(), Timer::Reset(), and TERMINATE.

Referenced by AbstractStaticLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::Solve(), AbstractDynamicLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::Solve(), SimpleNewtonNonlinearSolver::Solve(), and OdeLinearSystemSolver::SolveOneTimeStep().

void LinearSystem::SetRhsVectorElement	(	PetscInt	row,
		double	value
	)

Set an element of the right-hand side vector to a given value.

Parameters:

	row	the row index
	value	the value to set this entry

Definition at line 341 of file LinearSystem.cpp.

References mRhsVector, and PetscVecTools::SetElement().

Referenced by BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::ApplyDirichletToLinearProblem(), and AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >::FinaliseLinearSystem().

void LinearSystem::AddToRhsVectorElement	(	PetscInt	row,
		double	value
	)

Add a value to an element of the right-hand side vector.

Parameters:

	row	the row index
	value	the value to set this entry

Definition at line 346 of file LinearSystem.cpp.

References PetscVecTools::AddToElement(), and mRhsVector.

unsigned LinearSystem::GetSize ( ) const

Get method for mSize.

Definition at line 403 of file LinearSystem.cpp.

References mSize.

Referenced by BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::ApplyDirichletToLinearProblem(), AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >::FinaliseForBath(), and AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >::FinaliseLinearSystem().

void LinearSystem::SetNullBasis	(	Vec	nullbasis[],
		unsigned	numberOfBases
	)

Set the null basis of the linear system. In debug mode we test for orthonormality and throw EXCEPTIONs:

each direction is of unit length (to within a tolerance)
the directions are mutually orthogonal (to within a tolerance) Note that in NDEBUG (optimised mode) these tests are skipped and the parameters are passed directly into the LinearSystem.

Parameters:

	nullbasis	an array PETSc vectors containing orthogonal directions in the nullspace
	numberOfBases	the number of directions (size of nullbasis array)

Definition at line 408 of file LinearSystem.cpp.

References EXCEPTION, and mMatNullSpace.

Referenced by AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >::FinaliseLinearSystem().

void LinearSystem::RemoveNullSpace ( )

Remove the null space from the linear system.

Use for example if Dirichlet BC are applied to a singular system and, therefore, there's no null space anymore.

Definition at line 448 of file LinearSystem.cpp.

References mKspIsSetup, mKspSolver, and mMatNullSpace.

Referenced by BidomainProblem< DIM >::AtBeginningOfTimestep().

Vec & LinearSystem::rGetRhsVector ( )

Get access to the RHS vector directly. Shouldn't generally need to be called.

Definition at line 491 of file LinearSystem.cpp.

References mRhsVector.

Vec LinearSystem::GetRhsVector ( ) const

Get access to the RHS vector for archiving

Definition at line 496 of file LinearSystem.cpp.

References mRhsVector.

Mat & LinearSystem::rGetLhsMatrix ( )

Get access to the LHS matrix directly. Shouldn't generally need to be called.

Definition at line 501 of file LinearSystem.cpp.

References mLhsMatrix.

Referenced by AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >::FinaliseForBath(), OdeLinearSystemSolver::rGetLhsMatrix(), AbstractAssemblerSolverHybrid< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, INTERPOLATION_LEVEL >::SetupGivenLinearSystem(), OperatorSplittingMonodomainSolver< ELEMENT_DIM, SPACE_DIM >::SetupLinearSystem(), MatrixBasedMonodomainSolver< ELEMENT_DIM, SPACE_DIM >::SetupLinearSystem(), MatrixBasedBidomainSolver< ELEMENT_DIM, SPACE_DIM >::SetupLinearSystem(), BasicMonodomainSolver< ELEMENT_DIM, SPACE_DIM >::SetupLinearSystem(), BasicBidomainSolver< ELEMENT_DIM, SPACE_DIM >::SetupLinearSystem(), SimpleNewtonNonlinearSolver::Solve(), and OdeLinearSystemSolver::SolveOneTimeStep().

Mat LinearSystem::GetLhsMatrix ( ) const

Get access to the LHS matrix for archiving

Definition at line 506 of file LinearSystem.cpp.

References mLhsMatrix.

Referenced by AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >::FinaliseForBath().

Mat & LinearSystem::rGetPrecondMatrix ( )

Get access to the matrix used for preconditioning.

Definition at line 511 of file LinearSystem.cpp.

References EXCEPTION, mPrecondMatrix, and mPrecondMatrixIsNotLhs.

Referenced by MatrixBasedMonodomainSolver< ELEMENT_DIM, SPACE_DIM >::SetupLinearSystem().

Vec & LinearSystem::rGetDirichletBoundaryConditionsVector ( )

Get access to the dirichlet boundary conditions vector.

Should only be used by the BoundaryConditionsContainer.

Definition at line 521 of file LinearSystem.cpp.

References mDirichletBoundaryConditionsVector.

Referenced by BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::ApplyDirichletToLinearProblem().

void LinearSystem::GetOwnershipRange	(	PetscInt &	lo,
		PetscInt &	hi
	)

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

Parameters:

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

Definition at line 464 of file LinearSystem.cpp.

References mOwnershipRangeHi, and mOwnershipRangeLo.

Referenced by BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::ApplyDirichletToLinearProblem(), and AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >::FinaliseForBath().

double LinearSystem::GetMatrixElement	(	PetscInt	row,
		PetscInt	col
	)

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

Parameters:

	row	the row index
	col	the column index

Definition at line 470 of file LinearSystem.cpp.

References PetscMatTools::GetElement(), and mLhsMatrix.

Referenced by AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >::FinaliseForBath().

double LinearSystem::GetRhsVectorElement ( PetscInt row )

Return an element of the RHS vector. May only be called for elements you own.

Parameters:

row

the row index

Definition at line 475 of file LinearSystem.cpp.

References PetscVecTools::GetElement(), and mRhsVector.

unsigned LinearSystem::GetNumIterations ( ) const

Return the number of iterations taken by the last Solve()

Definition at line 480 of file LinearSystem.cpp.

References mKspIsSetup, and mKspSolver.

template<size_t MATRIX_SIZE>

void LinearSystem::AddLhsMultipleValues	(	unsigned *	matrixRowAndColIndices,
		c_matrix< double, MATRIX_SIZE, MATRIX_SIZE > &	rSmallMatrix
	)			`[inline]`

Add multiple values to the matrix of linear system.

Parameters:

	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 531 of file LinearSystem.hpp.

References PetscMatTools::AddMultipleValues(), and mLhsMatrix.

template<size_t VECTOR_SIZE>

void LinearSystem::AddRhsMultipleValues	(	unsigned *	vectorIndices,
		c_vector< double, VECTOR_SIZE > &	smallVector
	)			`[inline]`

Add multiple values to the RHS vector.

Parameters:

	vectorIndices	mapping from index of the ublas vector (see param below) to index of the vector of this linear system
	smallVector	Ublas vector 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 546 of file LinearSystem.hpp.

References PetscVecTools::AddMultipleValues(), and mRhsVector.

void LinearSystem::SetPrecondMatrixIsDifferentFromLhs ( bool precondIsDifferent = true )

Set method for mPrecondMatrixIsNotLhs.

Parameters:

precondIsDifferent

whether the matrix used for preconditioning is the same as the LHS.

Definition at line 1116 of file LinearSystem.cpp.

References mOwnershipRangeHi, mOwnershipRangeLo, mPrecondMatrix, mPrecondMatrixIsNotLhs, mRowPreallocation, mSize, NEVER_REACHED, and PetscTools::SetupMat().

Referenced by MatrixBasedMonodomainSolver< ELEMENT_DIM, SPACE_DIM >::SetupLinearSystem().

void LinearSystem::SetUseFixedNumberIterations	(	bool	useFixedNumberIterations = `true`,
		unsigned	evaluateNumItsEveryNSolves = `UINT_MAX`
	)

Set method for mUseFixedNumberIterations

Parameters:

	useFixedNumberIterations	whether to use fixed number of iterations
	evaluateNumItsEveryNSolves	tells LinearSystem to perform a solve with convergence-based stop criteria every n solves to decide how many iterations perform for the next n-1 solves. Default is perfoming a single evaluation at the beginning of the simulation.

Definition at line 1141 of file LinearSystem.cpp.

References mEvaluateNumItsEveryNSolves, and mUseFixedNumberIterations.

Referenced by OperatorSplittingMonodomainSolver< ELEMENT_DIM, SPACE_DIM >::InitialiseForSolve(), AbstractMonodomainSolver< ELEMENT_DIM, SPACE_DIM >::InitialiseForSolve(), and AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >::InitialiseForSolve().

void LinearSystem::ResetKspSolver ( )

Method to regenerate all KSP objects, including the solver and the preconditioner (e.g. after changing the PDE time step when using time adaptivity).

Todo:: #1695 Store this number in a member variable.

Definition at line 1148 of file LinearSystem.cpp.

References mForceSpectrumReevaluation, mKspIsSetup, and mKspSolver.

Referenced by AbstractDynamicLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::Solve().

Friends And Related Function Documentation

friend class boost::serialization::access [friend]

Needed for serialization.

Definition at line 148 of file LinearSystem.hpp.

Member Data Documentation

Mat LinearSystem::mLhsMatrix [private]

The left-hand side matrix.

Definition at line 69 of file LinearSystem.hpp.

Referenced by AddLhsMultipleValues(), AddToMatrixElement(), AssembleFinalLhsMatrix(), AssembleIntermediateLhsMatrix(), DisplayMatrix(), GetLhsMatrix(), GetMatrixElement(), GetMatrixRowDistributed(), IsMatrixSymmetric(), LinearSystem(), rGetLhsMatrix(), SetMatrixElement(), SetMatrixIsSymmetric(), SetMatrixRow(), Solve(), ZeroLhsMatrix(), ZeroMatrixColumn(), ZeroMatrixRowsAndColumnsWithValueOnDiagonal(), ZeroMatrixRowsWithValueOnDiagonal(), and ~LinearSystem().

Mat LinearSystem::mPrecondMatrix [private]

The matrix used for preconditioning.

Definition at line 70 of file LinearSystem.hpp.

Referenced by AssembleFinalPrecondMatrix(), rGetPrecondMatrix(), SetPrecondMatrixIsDifferentFromLhs(), Solve(), and ~LinearSystem().

Vec LinearSystem::mRhsVector [private]

The right-hand side vector.

Definition at line 71 of file LinearSystem.hpp.

Referenced by AddRhsMultipleValues(), AddToRhsVectorElement(), AssembleRhsVector(), DisplayRhs(), GetRhsVector(), GetRhsVectorElement(), LinearSystem(), rGetRhsVector(), SetRhsVectorElement(), Solve(), ZeroRhsVector(), and ~LinearSystem().

PetscInt LinearSystem::mSize [private]

The size of the linear system.

Definition at line 72 of file LinearSystem.hpp.

Referenced by GetSize(), LinearSystem(), SetPrecondMatrixIsDifferentFromLhs(), and Solve().

PetscInt LinearSystem::mOwnershipRangeLo [private]

Todo:: Verify claim that ownership range for Vec and Mat is same. This should only matter for efficiency if the claim is false.

For parallel code. Stores lowest index of vectors and lowest row of matrix stored locally.

Definition at line 78 of file LinearSystem.hpp.

Referenced by GetOwnershipRange(), LinearSystem(), and SetPrecondMatrixIsDifferentFromLhs().

PetscInt LinearSystem::mOwnershipRangeHi [private]

Stores one more than the highest index stored locally.

Definition at line 79 of file LinearSystem.hpp.

Referenced by GetOwnershipRange(), LinearSystem(), and SetPrecondMatrixIsDifferentFromLhs().

MatNullSpace LinearSystem::mMatNullSpace [private]

PETSc null matrix.

Definition at line 81 of file LinearSystem.hpp.

Referenced by RemoveNullSpace(), SetNullBasis(), Solve(), and ~LinearSystem().

bool LinearSystem::mDestroyMatAndVec [private]

Whether we need to destroy the PETSc matrix and vector in our destructor

Definition at line 84 of file LinearSystem.hpp.

Referenced by ~LinearSystem().

KSP LinearSystem::mKspSolver [private]

The PETSc linear solver object

Definition at line 86 of file LinearSystem.hpp.

Referenced by GetNumIterations(), RemoveNullSpace(), ResetKspSolver(), SetAbsoluteTolerance(), SetKspType(), SetPcType(), SetRelativeTolerance(), Solve(), and ~LinearSystem().

bool LinearSystem::mKspIsSetup [private]

Used by Solve method to track whether KSP has been used.

Definition at line 87 of file LinearSystem.hpp.

Referenced by GetNumIterations(), RemoveNullSpace(), ResetKspSolver(), SetAbsoluteTolerance(), SetKspType(), SetPcType(), SetRelativeTolerance(), Solve(), and ~LinearSystem().

double LinearSystem::mNonZerosUsed [private]

Yes, it really is stored as a double.

Definition at line 88 of file LinearSystem.hpp.

Referenced by serialize(), and Solve().

bool LinearSystem::mMatrixIsConstant [private]

Whether the matrix is unchanged each time Solve() is called

Definition at line 89 of file LinearSystem.hpp.

Referenced by serialize(), SetMatrixIsConstant(), and Solve().

double LinearSystem::mTolerance [private]

absolute or relative tolerance of the KSP solver

Definition at line 90 of file LinearSystem.hpp.

Referenced by serialize(), SetAbsoluteTolerance(), SetRelativeTolerance(), and Solve().

bool LinearSystem::mUseAbsoluteTolerance [private]

Sets either absolute or relative tolerance of the KSP solver. Default is to false

Definition at line 95 of file LinearSystem.hpp.

Referenced by serialize(), SetAbsoluteTolerance(), SetRelativeTolerance(), and Solve().

std::string LinearSystem::mKspType [private]

KSP solver type (see PETSc KSPSetType() )

Definition at line 96 of file LinearSystem.hpp.

Referenced by LinearSystem(), serialize(), SetKspType(), and Solve().

std::string LinearSystem::mPcType [private]

Preconditioner type (see PETSc PCSetType() )

Definition at line 97 of file LinearSystem.hpp.

Referenced by LinearSystem(), serialize(), SetPcType(), and Solve().

Vec LinearSystem::mDirichletBoundaryConditionsVector [private]

Storage for efficient application of Dirichlet BCs, see AbstractBoundaryConditionsContainer

Definition at line 99 of file LinearSystem.hpp.

Referenced by rGetDirichletBoundaryConditionsVector(), and ~LinearSystem().

PCBlockDiagonal* LinearSystem::mpBlockDiagonalPC [private]

Todo:: : #1082 Create an abstract class for the preconditioners and use a single pointer

Stores a pointer to a purpose-build preconditioner

Definition at line 103 of file LinearSystem.hpp.

Referenced by SetPcType(), Solve(), and ~LinearSystem().

PCLDUFactorisation* LinearSystem::mpLDUFactorisationPC [private]

Stores a pointer to a purpose-build preconditioner

Definition at line 105 of file LinearSystem.hpp.

Referenced by SetPcType(), Solve(), and ~LinearSystem().

PCTwoLevelsBlockDiagonal* LinearSystem::mpTwoLevelsBlockDiagonalPC [private]

Stores a pointer to a purpose-build preconditioner

Definition at line 107 of file LinearSystem.hpp.

Referenced by SetPcType(), Solve(), and ~LinearSystem().

boost::shared_ptr<std::vector<PetscInt> > LinearSystem::mpBathNodes [private]

Pointer to vector containing a list of bath nodes

Definition at line 110 of file LinearSystem.hpp.

Referenced by SetPcType(), and Solve().

bool LinearSystem::mPrecondMatrixIsNotLhs [private]

Whether the matrix used for preconditioning is the same as the LHS

Definition at line 113 of file LinearSystem.hpp.

Referenced by rGetPrecondMatrix(), SetPrecondMatrixIsDifferentFromLhs(), Solve(), and ~LinearSystem().

unsigned LinearSystem::mRowPreallocation [private]

The max number of nonzero entries expected on a LHS row

Definition at line 116 of file LinearSystem.hpp.

Referenced by LinearSystem(), and SetPrecondMatrixIsDifferentFromLhs().

bool LinearSystem::mUseFixedNumberIterations [private]

Whether to use fixed number of iterations

Definition at line 119 of file LinearSystem.hpp.

Referenced by SetUseFixedNumberIterations(), and Solve().

unsigned LinearSystem::mEvaluateNumItsEveryNSolves [private]

When using fixed number of iterations, a solve with residual-based stop criteria will be performed every mEvaluateNumItsEveryNSolves solves to decide how many iterations perform for the next mEvaluateNumItsEveryNSolves-1 solves

Definition at line 126 of file LinearSystem.hpp.

Referenced by SetUseFixedNumberIterations(), and Solve().

void* LinearSystem::mpConvergenceTestContext [private]

Context for KSPDefaultConverged()

Definition at line 129 of file LinearSystem.hpp.

Referenced by Solve(), and ~LinearSystem().

unsigned LinearSystem::mNumSolves [private]

Number of solves performed since the current object was created

Definition at line 132 of file LinearSystem.hpp.

Referenced by LinearSystem(), Solve(), and ~LinearSystem().

PetscReal LinearSystem::mEigMin [private]

Preconditioned operator smallest eigenvalue

Definition at line 135 of file LinearSystem.hpp.

Referenced by Solve().

PetscReal LinearSystem::mEigMax [private]

Preconditioned operator largest eigenvalue

Definition at line 138 of file LinearSystem.hpp.

Referenced by Solve().

bool LinearSystem::mForceSpectrumReevaluation [private]

Under certain circunstances you have to reevaluate the spectrum before the k*n-th, k=0,1,..., iteration

Definition at line 141 of file LinearSystem.hpp.

Referenced by ResetKspSolver(), and Solve().

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

linalg/src/LinearSystem.hpp
linalg/src/LinearSystem.cpp


Public Member Functions
	LinearSystem (PetscInt lhsVectorSize, unsigned rowPreallocation=UINT_MAX)
	LinearSystem (Vec templateVector, unsigned rowPreallocation)
	LinearSystem (Vec residualVector, Mat jacobianMatrix)
	LinearSystem (PetscInt lhsVectorSize, Mat lhsMatrix, Vec rhsVector)
	~LinearSystem ()
void	SetMatrixElement (PetscInt row, PetscInt col, double value)
void	AddToMatrixElement (PetscInt row, PetscInt col, double value)
void	AssembleFinalLinearSystem ()
void	AssembleIntermediateLinearSystem ()
void	AssembleFinalLhsMatrix ()
void	AssembleFinalPrecondMatrix ()
void	AssembleIntermediateLhsMatrix ()
void	AssembleRhsVector ()
void	SetMatrixIsSymmetric (bool isSymmetric=true)
bool	IsMatrixSymmetric ()
void	SetMatrixIsConstant (bool matrixIsConstant)
void	SetRelativeTolerance (double relativeTolerance)
void	SetAbsoluteTolerance (double absoluteTolerance)
void	SetKspType (const char *kspType)
void	SetPcType (const char *pcType, boost::shared_ptr< std::vector< PetscInt > > pBathNodes=boost::shared_ptr< std::vector< PetscInt > >())
void	DisplayMatrix ()
void	DisplayRhs ()
void	SetMatrixRow (PetscInt row, double value)
Vec	GetMatrixRowDistributed (unsigned rowIndex)
void	ZeroMatrixRowsWithValueOnDiagonal (std::vector< unsigned > &rRows, double diagonalValue)
void	ZeroMatrixRowsAndColumnsWithValueOnDiagonal (std::vector< unsigned > &rRowColIndices, double diagonalValue)
void	ZeroMatrixColumn (PetscInt col)
void	ZeroLhsMatrix ()
void	ZeroRhsVector ()
void	ZeroLinearSystem ()
Vec	Solve (Vec lhsGuess=NULL)
void	SetRhsVectorElement (PetscInt row, double value)
void	AddToRhsVectorElement (PetscInt row, double value)
unsigned	GetSize () const
void	SetNullBasis (Vec nullbasis[], unsigned numberOfBases)
void	RemoveNullSpace ()
Vec &	rGetRhsVector ()
Vec	GetRhsVector () const
Mat &	rGetLhsMatrix ()
Mat	GetLhsMatrix () const
Mat &	rGetPrecondMatrix ()
Vec &	rGetDirichletBoundaryConditionsVector ()
void	GetOwnershipRange (PetscInt &lo, PetscInt &hi)
double	GetMatrixElement (PetscInt row, PetscInt col)
double	GetRhsVectorElement (PetscInt row)
unsigned	GetNumIterations () const
template<size_t MATRIX_SIZE>
void	AddLhsMultipleValues (unsigned *matrixRowAndColIndices, c_matrix< double, MATRIX_SIZE, MATRIX_SIZE > &rSmallMatrix)
template<size_t VECTOR_SIZE>
void	AddRhsMultipleValues (unsigned *vectorIndices, c_vector< double, VECTOR_SIZE > &smallVector)
void	SetPrecondMatrixIsDifferentFromLhs (bool precondIsDifferent=true)
void	SetUseFixedNumberIterations (bool useFixedNumberIterations=true, unsigned evaluateNumItsEveryNSolves=UINT_MAX)
void	ResetKspSolver ()
Private Member Functions
template<class Archive>
void	serialize (Archive &archive, const unsigned int version)
Private Attributes
Mat	mLhsMatrix
Mat	mPrecondMatrix
Vec	mRhsVector
PetscInt	mSize
PetscInt	mOwnershipRangeLo
PetscInt	mOwnershipRangeHi
MatNullSpace	mMatNullSpace
bool	mDestroyMatAndVec
KSP	mKspSolver
bool	mKspIsSetup
double	mNonZerosUsed
bool	mMatrixIsConstant
double	mTolerance
bool	mUseAbsoluteTolerance
std::string	mKspType
std::string	mPcType
Vec	mDirichletBoundaryConditionsVector
PCBlockDiagonal *	mpBlockDiagonalPC
PCLDUFactorisation *	mpLDUFactorisationPC
PCTwoLevelsBlockDiagonal *	mpTwoLevelsBlockDiagonalPC
boost::shared_ptr< std::vector < PetscInt > >	mpBathNodes
bool	mPrecondMatrixIsNotLhs
unsigned	mRowPreallocation
bool	mUseFixedNumberIterations
unsigned	mEvaluateNumItsEveryNSolves
void *	mpConvergenceTestContext
unsigned	mNumSolves
PetscReal	mEigMin
PetscReal	mEigMax
bool	mForceSpectrumReevaluation
Friends
class	TestLinearSystem
class	TestPCBlockDiagonal
class	TestPCTwoLevelsBlockDiagonal
class	TestPCLDUFactorisation
class	TestChebyshevIteration
class	boost::serialization::access