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 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 row_index)

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

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)

Private Member Functions

template<class Archive>

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

Private Attributes

Mat mLhsMatrix

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

Friends

class TestLinearSystem

class TestPCBlockDiagonal

class TestPCTwoLevelsBlockDiagonal

class TestPCLDUFactorisation

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 57 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 43 of file LinearSystem.cpp.

References PetscTools::CreateVec(), EXCEPTION, mKspType, mLhsMatrix, mOwnershipRangeHi, mOwnershipRangeLo, mPcType, mRhsVector, 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 118 of file LinearSystem.cpp.

References mKspType, mLhsMatrix, mOwnershipRangeHi, mOwnershipRangeLo, mPcType, mRhsVector, 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 150 of file LinearSystem.cpp.

References mKspType, mLhsMatrix, mOwnershipRangeHi, mOwnershipRangeLo, mPcType, mRhsVector, 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 89 of file LinearSystem.cpp.

References mLhsMatrix, mOwnershipRangeHi, mOwnershipRangeLo, and mRhsVector.

LinearSystem::~LinearSystem ( )

Destructor.

Todo:: Never tested in linalg component

Definition at line 196 of file LinearSystem.cpp.

References PetscTools::AmMaster(), mDestroyMatAndVec, mDirichletBoundaryConditionsVector, mKspIsSetup, mKspSolver, mLhsMatrix, mMatNullSpace, mpBlockDiagonalPC, mpLDUFactorisationPC, 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 123 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 241 of file LinearSystem.cpp.

References mLhsMatrix, mOwnershipRangeHi, and mOwnershipRangeLo.

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

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 249 of file LinearSystem.cpp.

References mLhsMatrix, mOwnershipRangeHi, and mOwnershipRangeLo.

void LinearSystem::AssembleFinalLinearSystem ( )

Call this before Solve().

This calls AssembleFinalLhsMatrix() and AssembleRhsVector().

Definition at line 257 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 263 of file LinearSystem.cpp.

References AssembleIntermediateLhsMatrix(), and AssembleRhsVector().

void LinearSystem::AssembleFinalLhsMatrix ( )

Sets up the PETSc matrix left-hand-side mLhsMatrix

Definition at line 269 of file LinearSystem.cpp.

References mLhsMatrix.

Referenced by AssembleFinalLinearSystem(), NonlinearElasticitySolver< DIM >::AssembleSystem(), AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >::FinaliseLinearSystem(), AbstractAssemblerSolverHybrid< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, INTERPOLATION_LEVEL >::SetupGivenLinearSystem(), 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::AssembleIntermediateLhsMatrix ( )

Sets up the PETSc matrix left-hand-side mLhsMatrix

Definition at line 275 of file LinearSystem.cpp.

References mLhsMatrix.

Referenced by AssembleIntermediateLinearSystem(), NonlinearElasticitySolver< DIM >::AssembleSystem(), 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 281 of file LinearSystem.cpp.

References mRhsVector.

Referenced by AssembleFinalLinearSystem(), AssembleIntermediateLinearSystem(), NonlinearElasticitySolver< DIM >::AssembleSystem(), AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >::FinaliseLinearSystem(), AbstractAssemblerSolverHybrid< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, INTERPOLATION_LEVEL >::SetupGivenLinearSystem(), 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 636 of file LinearSystem.cpp.

References mLhsMatrix.

Referenced by SimpleLinearEllipticSolver< 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 664 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 675 of file LinearSystem.cpp.

References mMatrixIsConstant.

void LinearSystem::SetRelativeTolerance ( double relativeTolerance )

Set the relative tolerance.

Parameters:

relativeTolerance

the relative tolerance

Definition at line 680 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 690 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::SetKspType ( const char * kspType )

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

Parameters:

kspType

the KSP solver type

Definition at line 700 of file LinearSystem.cpp.

References mKspIsSetup, mKspSolver, and mKspType.

Referenced by AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >::FinaliseLinearSystem(), SimpleLinearEllipticSolver< 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 710 of file LinearSystem.cpp.

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

Referenced by 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 303 of file LinearSystem.cpp.

References mLhsMatrix.

void LinearSystem::DisplayRhs ( )

Display the right-hand side vector.

Definition at line 308 of file LinearSystem.cpp.

References 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 313 of file LinearSystem.cpp.

References mLhsMatrix, mOwnershipRangeHi, mOwnershipRangeLo, and SetMatrixElement().

Vec LinearSystem::GetMatrixRowDistributed ( unsigned row_index )

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

Parameters:

row_index

the row index

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

Definition at line 326 of file LinearSystem.cpp.

References mLhsMatrix, mOwnershipRangeHi, mOwnershipRangeLo, and mRhsVector.

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 356 of file LinearSystem.cpp.

References mLhsMatrix.

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

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 392 of file LinearSystem.cpp.

References GetMatrixElement(), mLhsMatrix, mOwnershipRangeHi, mOwnershipRangeLo, and ZeroMatrixRowsWithValueOnDiagonal().

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 448 of file LinearSystem.cpp.

References GetMatrixElement(), mLhsMatrix, mOwnershipRangeHi, and mOwnershipRangeLo.

void LinearSystem::ZeroLhsMatrix ( )

Zero all entries of the left-hand side matrix.

Definition at line 494 of file LinearSystem.cpp.

References mLhsMatrix.

Referenced by NonlinearElasticitySolver< DIM >::AssembleSystem(), and ZeroLinearSystem().

void LinearSystem::ZeroRhsVector ( )

Zero all entries of the right-hand side vector.

Definition at line 483 of file LinearSystem.cpp.

References mOwnershipRangeHi, mOwnershipRangeLo, and mRhsVector.

Referenced by NonlinearElasticitySolver< DIM >::AssembleSystem(), MatrixBasedMonodomainSolver< ELEMENT_DIM, SPACE_DIM >::SetupLinearSystem(), MatrixBasedBidomainSolver< ELEMENT_DIM, SPACE_DIM >::SetupLinearSystem(), and ZeroLinearSystem().

void LinearSystem::ZeroLinearSystem ( )

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

Definition at line 499 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?

Definition at line 770 of file LinearSystem.cpp.

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

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

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 287 of file LinearSystem.cpp.

References mOwnershipRangeHi, mOwnershipRangeLo, and mRhsVector.

Referenced by AbstractNonlinearElasticitySolver< DIM >::ApplyBoundaryConditions(), 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 295 of file LinearSystem.cpp.

References mOwnershipRangeHi, mOwnershipRangeLo, and mRhsVector.

unsigned LinearSystem::GetSize ( ) const

Get method for mSize.

Definition at line 505 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 510 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 550 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 611 of file LinearSystem.cpp.

References mRhsVector.

Vec LinearSystem::GetRhsVector ( ) const

Get access to the RHS vector for archiving

Definition at line 616 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 621 of file LinearSystem.cpp.

References mLhsMatrix.

Referenced by NonlinearElasticitySolver< DIM >::AllocateMatrixMemory(), AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >::FinaliseForBath(), AbstractAssemblerSolverHybrid< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, INTERPOLATION_LEVEL >::SetupGivenLinearSystem(), 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 AbstractNonlinearElasticitySolver< DIM >::TakeNewtonStep().

Mat LinearSystem::GetLhsMatrix ( ) const

Get access to the LHS matrix for archiving

Definition at line 626 of file LinearSystem.cpp.

References mLhsMatrix.

Vec & LinearSystem::rGetDirichletBoundaryConditionsVector ( )

Get access to the dirichlet boundary conditions vector.

Should only be used by the BoundaryConditionsContainer.

Definition at line 631 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 566 of file LinearSystem.cpp.

References mOwnershipRangeHi, and mOwnershipRangeLo.

Referenced by NonlinearElasticitySolver< DIM >::AllocateMatrixMemory(), 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 572 of file LinearSystem.cpp.

References mLhsMatrix, mOwnershipRangeHi, and mOwnershipRangeLo.

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

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 587 of file LinearSystem.cpp.

References mOwnershipRangeHi, mOwnershipRangeLo, and mRhsVector.

unsigned LinearSystem::GetNumIterations ( ) const

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

Definition at line 600 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 488 of file LinearSystem.hpp.

References mLhsMatrix, mOwnershipRangeHi, and mOwnershipRangeLo.

Referenced by NonlinearElasticitySolver< DIM >::AssembleSystem().

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 551 of file LinearSystem.hpp.

References mOwnershipRangeHi, mOwnershipRangeLo, and mRhsVector.

Referenced by NonlinearElasticitySolver< DIM >::AssembleSystem().

Friends And Related Function Documentation

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

Needed for serialization.

Definition at line 115 of file LinearSystem.hpp.

Member Data Documentation

Mat LinearSystem::mLhsMatrix [private]

The left-hand side matrix.

Definition at line 66 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().

Vec LinearSystem::mRhsVector [private]

The right-hand side vector.

Definition at line 67 of file LinearSystem.hpp.

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

PetscInt LinearSystem::mSize [private]

The size of the linear system.

Definition at line 68 of file LinearSystem.hpp.

Referenced by GetSize(), LinearSystem(), 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 74 of file LinearSystem.hpp.

Referenced by AddLhsMultipleValues(), AddRhsMultipleValues(), AddToMatrixElement(), AddToRhsVectorElement(), GetMatrixElement(), GetMatrixRowDistributed(), GetOwnershipRange(), GetRhsVectorElement(), LinearSystem(), SetMatrixElement(), SetMatrixRow(), SetRhsVectorElement(), ZeroMatrixColumn(), ZeroMatrixRowsAndColumnsWithValueOnDiagonal(), and ZeroRhsVector().

PetscInt LinearSystem::mOwnershipRangeHi [private]

Stores one more than the highest index stored locally.

Definition at line 75 of file LinearSystem.hpp.

Referenced by AddLhsMultipleValues(), AddRhsMultipleValues(), AddToMatrixElement(), AddToRhsVectorElement(), GetMatrixElement(), GetMatrixRowDistributed(), GetOwnershipRange(), GetRhsVectorElement(), LinearSystem(), SetMatrixElement(), SetMatrixRow(), SetRhsVectorElement(), ZeroMatrixColumn(), ZeroMatrixRowsAndColumnsWithValueOnDiagonal(), and ZeroRhsVector().

MatNullSpace LinearSystem::mMatNullSpace [private]

PETSc null matrix.

Definition at line 77 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 80 of file LinearSystem.hpp.

Referenced by ~LinearSystem().

KSP LinearSystem::mKspSolver [private]

The PETSc linear solver object

Definition at line 82 of file LinearSystem.hpp.

Referenced by GetNumIterations(), RemoveNullSpace(), 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 83 of file LinearSystem.hpp.

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

double LinearSystem::mNonZerosUsed [private]

Yes, it really is stored as a double.

Definition at line 84 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 85 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 86 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 91 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 92 of file LinearSystem.hpp.

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

std::string LinearSystem::mPcType [private]

Preconditioner type (see PETSc PCSetType() )

Definition at line 93 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 95 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 99 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 101 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 103 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 106 of file LinearSystem.hpp.

Referenced by SetPcType(), and Solve().

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

linalg/src/common/LinearSystem.hpp
linalg/src/common/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	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 row_index)
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
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)
Private Member Functions
template<class Archive>
void	serialize (Archive &archive, const unsigned int version)
Private Attributes
Mat	mLhsMatrix
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
Friends
class	TestLinearSystem
class	TestPCBlockDiagonal
class	TestPCTwoLevelsBlockDiagonal
class	TestPCLDUFactorisation
class	boost::serialization::access