LinearSystem Class Reference

#include <LinearSystem.hpp>

Collaboration diagram for LinearSystem:

Public Member Functions
	LinearSystem (PetscInt lhsVectorSize, MatType matType=(MatType) MATMPIAIJ)
	LinearSystem (Vec templateVector)
	LinearSystem (Vec residualVector, Mat jacobianMatrix)
	LinearSystem (PetscInt lhsVectorSize, Mat lhsMatrix, Vec rhsVector, MatType matType=(MatType) MATMPIAIJ)
	~LinearSystem ()
void	SetupVectorAndMatrix (MatType matType)
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)
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
Friends
class	TestLinearSystem
class	TestPCBlockDiagonal
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 55 of file LinearSystem.hpp.

Constructor & Destructor Documentation

LinearSystem::LinearSystem	(	PetscInt	lhsVectorSize,
		MatType	matType = `(MatType) MATMPIAIJ`
	)

Constructor.

Parameters:

	lhsVectorSize	the size of the LHS vector
	matType	the type of matrix (defaults to MATMPIAIJ)

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

Definition at line 43 of file LinearSystem.cpp.

References mKspType, mPcType, and SetupVectorAndMatrix().

LinearSystem::LinearSystem ( Vec templateVector )

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

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

Definition at line 96 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 assembler, these are gonna be the default solver and preconditioner. Not consitent with ChasteDefaults.xml though...

Definition at line 126 of file LinearSystem.cpp.

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

LinearSystem::LinearSystem	(	PetscInt	lhsVectorSize,
		Mat	lhsMatrix,
		Vec	rhsVector,
		MatType	matType = `(MatType) MATMPIAIJ`
	)

Alternative constructor for archiving.

Parameters:

	lhsVectorSize	the size of the LHS vector
	lhsMatrix	the RHS matrix
	rhsVector	the RHS vector
	matType	the type of matrix (defaults to MATMPIAIJ)

Definition at line 70 of file LinearSystem.cpp.

References mLhsMatrix, mOwnershipRangeHi, mOwnershipRangeLo, and mRhsVector.

LinearSystem::~LinearSystem ( )

Destructor.

Todo:: Never tested in linalg component

Definition at line 170 of file LinearSystem.cpp.

References mDestroyMatAndVec, mDirichletBoundaryConditionsVector, mKspIsSetup, mKspSolver, mLhsMatrix, mMatNullSpace, mpBlockDiagonalPC, mpLDUFactorisationPC, and mRhsVector.

Member Function Documentation

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 479 of file LinearSystem.hpp.

References mLhsMatrix, mOwnershipRangeHi, and mOwnershipRangeLo.

Referenced by NonlinearElasticityAssembler< DIM >::AssembleSystem(), and AbstractStaticAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, NON_HEART, CONCRETE >::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 542 of file LinearSystem.hpp.

References mOwnershipRangeHi, mOwnershipRangeLo, and mRhsVector.

Referenced by NonlinearElasticityAssembler< DIM >::AssembleSystem(), and AbstractStaticAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, NON_HEART, CONCRETE >::AssembleSystem().

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 236 of file LinearSystem.cpp.

References mLhsMatrix, mOwnershipRangeHi, and mOwnershipRangeLo.

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 282 of file LinearSystem.cpp.

References mOwnershipRangeHi, mOwnershipRangeLo, and mRhsVector.

void LinearSystem::AssembleFinalLhsMatrix ( )

Sets up the PETSc matrix left-hand-side mLhsMatrix

Definition at line 256 of file LinearSystem.cpp.

References mLhsMatrix.

Referenced by AssembleFinalLinearSystem(), NonlinearElasticityAssembler< DIM >::AssembleSystem(), AbstractStaticAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, NON_HEART, CONCRETE >::AssembleSystem(), and BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::FinaliseAssembleSystem().

void LinearSystem::AssembleFinalLinearSystem ( )

Call this before Solve().

This calls AssembleFinalLhsMatrix() and AssembleRhsVector().

Definition at line 244 of file LinearSystem.cpp.

References AssembleFinalLhsMatrix(), and AssembleRhsVector().

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

void LinearSystem::AssembleIntermediateLhsMatrix ( )

Sets up the PETSc matrix left-hand-side mLhsMatrix

Definition at line 262 of file LinearSystem.cpp.

References mLhsMatrix.

Referenced by AssembleIntermediateLinearSystem(), NonlinearElasticityAssembler< DIM >::AssembleSystem(), and AbstractStaticAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, NON_HEART, CONCRETE >::AssembleSystem().

void LinearSystem::AssembleIntermediateLinearSystem ( )

Should be called before AddToMatrixElement.

This calls AssembleIntermediateLhsMatrix() and AssembleRhsVector().

Definition at line 250 of file LinearSystem.cpp.

References AssembleIntermediateLhsMatrix(), and AssembleRhsVector().

void LinearSystem::AssembleRhsVector ( )

Sets up the PETSc vector right-hand-side mRhsVector

Definition at line 268 of file LinearSystem.cpp.

References mRhsVector.

Referenced by AssembleFinalLinearSystem(), AssembleIntermediateLinearSystem(), NonlinearElasticityAssembler< DIM >::AssembleSystem(), AbstractStaticAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, NON_HEART, CONCRETE >::AssembleSystem(), and BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::FinaliseAssembleSystem().

void LinearSystem::DisplayMatrix ( )

Display the left-hand side matrix.

Definition at line 290 of file LinearSystem.cpp.

References mLhsMatrix.

void LinearSystem::DisplayRhs ( )

Display the right-hand side vector.

Definition at line 295 of file LinearSystem.cpp.

References mRhsVector.

Mat LinearSystem::GetLhsMatrix ( ) const

Get access to the LHS matrix for archiving

Definition at line 608 of file LinearSystem.cpp.

References mLhsMatrix.

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 554 of file LinearSystem.cpp.

References mLhsMatrix, mOwnershipRangeHi, and mOwnershipRangeLo.

Referenced by ZeroMatrixColumn(), and ZeroMatrixRowsAndColumnsWithValueOnDiagonal().

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 313 of file LinearSystem.cpp.

References mLhsMatrix, mOwnershipRangeHi, mOwnershipRangeLo, and mRhsVector.

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

unsigned LinearSystem::GetNumIterations ( ) const

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

Definition at line 582 of file LinearSystem.cpp.

References mKspIsSetup, and mKspSolver.

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 548 of file LinearSystem.cpp.

References mOwnershipRangeHi, and mOwnershipRangeLo.

Referenced by NonlinearElasticityAssembler< DIM >::AllocateMatrixMemory(), and BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::ApplyDirichletToLinearProblem().

Vec LinearSystem::GetRhsVector ( ) const

Get access to the RHS vector for archiving

Definition at line 598 of file LinearSystem.cpp.

References mRhsVector.

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 569 of file LinearSystem.cpp.

References mOwnershipRangeHi, mOwnershipRangeLo, and mRhsVector.

unsigned LinearSystem::GetSize ( ) const

Get method for mSize.

Definition at line 487 of file LinearSystem.cpp.

References mSize.

Referenced by BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::ApplyDirichletToLinearProblem(), AbstractStaticAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, NON_HEART, CONCRETE >::AssembleSystem(), and BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::FinaliseAssembleSystem().

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 646 of file LinearSystem.cpp.

References mLhsMatrix.

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

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 532 of file LinearSystem.cpp.

References mKspIsSetup, mKspSolver, and mMatNullSpace.

Vec & LinearSystem::rGetDirichletBoundaryConditionsVector ( )

Get access to the dirichlet boundary conditions vector.

Should only be used by the BoundaryConditionsContainer.

Definition at line 613 of file LinearSystem.cpp.

References mDirichletBoundaryConditionsVector.

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

Mat & LinearSystem::rGetLhsMatrix ( )

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

Definition at line 603 of file LinearSystem.cpp.

References mLhsMatrix.

Referenced by NonlinearElasticityAssembler< DIM >::AllocateMatrixMemory(), AbstractNonlinearAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, CONCRETE >::ApplyDirichletConditions(), AbstractStaticAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, NON_HEART, CONCRETE >::AssembleSystem(), MonodomainRhsMatrixAssembler< ELEMENT_DIM, SPACE_DIM >::GetMatrix(), BidomainWithBathRhsMatrixAssembler< DIM >::GetMatrix(), BidomainRhsMatrixAssembler< DIM >::GetMatrix(), SimpleNewtonNonlinearSolver::Solve(), and AbstractNonlinearElasticityAssembler< DIM >::TakeNewtonStep().

Vec & LinearSystem::rGetRhsVector ( )

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

Definition at line 593 of file LinearSystem.cpp.

References mRhsVector.

Referenced by AbstractNonlinearAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, CONCRETE >::ApplyDirichletConditions(), BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::ApplyDirichletToLinearProblem(), AbstractStaticAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, NON_HEART, CONCRETE >::AssembleSystem(), AbstractNonlinearElasticityAssembler< DIM >::CalculateResidualNorm(), SimpleNewtonNonlinearSolver::Solve(), and AbstractNonlinearElasticityAssembler< DIM >::TakeNewtonStep().

template<class Archive >

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

Archive the member variables.

Parameters:

	archive
	version

Definition at line 114 of file LinearSystem.hpp.

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

void LinearSystem::SetAbsoluteTolerance ( double absoluteTolerance )

Set the absolute tolerance.

Parameters:

absoluteTolerance

the absolute tolerance

Definition at line 672 of file LinearSystem.cpp.

References mKspIsSetup, mKspSolver, mTolerance, and mUseAbsoluteTolerance.

Referenced by MonodomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::InitialiseForSolve(), and BidomainDg0Assembler< 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 682 of file LinearSystem.cpp.

References mKspIsSetup, mKspSolver, and mKspType.

Referenced by BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::FinaliseAssembleSystem(), MonodomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::InitialiseForSolve(), and BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::InitialiseForSolve().

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 228 of file LinearSystem.cpp.

References mLhsMatrix, mOwnershipRangeHi, and mOwnershipRangeLo.

Referenced by BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::FinaliseAssembleSystem(), and SetMatrixRow().

void LinearSystem::SetMatrixIsConstant ( bool matrixIsConstant )

Set mMatrixIsConstant.

Parameters:

matrixIsConstant

whether the matrix is constant

Definition at line 657 of file LinearSystem.cpp.

References mMatrixIsConstant.

Referenced by AbstractLinearAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, NON_HEART, CONCRETE >::InitialiseForSolve().

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 618 of file LinearSystem.cpp.

References mLhsMatrix.

Referenced by MonodomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::InitialiseForSolve(), and BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::InitialiseForSolve().

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 300 of file LinearSystem.cpp.

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

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 492 of file LinearSystem.cpp.

References mMatNullSpace.

Referenced by BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::FinaliseAssembleSystem().

void LinearSystem::SetPcType ( const char * pcType )

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

Parameters:

pcType

the preconditioner type

Definition at line 692 of file LinearSystem.cpp.

References mKspIsSetup, mKspSolver, mpBlockDiagonalPC, mPcType, and mpLDUFactorisationPC.

Referenced by MonodomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::InitialiseForSolve(), and BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::InitialiseForSolve().

void LinearSystem::SetRelativeTolerance ( double relativeTolerance )

Set the relative tolerance.

Parameters:

relativeTolerance

the relative tolerance

Definition at line 662 of file LinearSystem.cpp.

References mKspIsSetup, mKspSolver, mTolerance, and mUseAbsoluteTolerance.

Referenced by MonodomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::InitialiseForSolve(), and BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::InitialiseForSolve().

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 274 of file LinearSystem.cpp.

References mOwnershipRangeHi, mOwnershipRangeLo, and mRhsVector.

Referenced by AbstractNonlinearElasticityAssembler< DIM >::ApplyBoundaryConditions(), BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::ApplyDirichletToLinearProblem(), and BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::FinaliseAssembleSystem().

void LinearSystem::SetupVectorAndMatrix ( MatType matType )

Helper method for the constructor. Initializes the LHS matrix and RHS vector.

Parameters:

matType

the type of matrix

Definition at line 217 of file LinearSystem.cpp.

References mLhsMatrix, mOwnershipRangeHi, mOwnershipRangeLo, mRhsVector, mSize, and PetscTools::SetupMat().

Referenced by LinearSystem().

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 725 of file LinearSystem.cpp.

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

Referenced by SimpleNewtonNonlinearSolver::Solve(), and AbstractLinearAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, NON_HEART, CONCRETE >::StaticSolve().

void LinearSystem::ZeroLhsMatrix ( )

Zero all entries of the left-hand side matrix.

Definition at line 476 of file LinearSystem.cpp.

References mLhsMatrix.

Referenced by NonlinearElasticityAssembler< DIM >::AssembleSystem(), AbstractStaticAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, NON_HEART, CONCRETE >::AssembleSystem(), and ZeroLinearSystem().

void LinearSystem::ZeroLinearSystem ( )

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

Definition at line 481 of file LinearSystem.cpp.

References ZeroLhsMatrix(), and ZeroRhsVector().

Referenced by SimpleNewtonNonlinearSolver::Solve().

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 430 of file LinearSystem.cpp.

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

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 375 of file LinearSystem.cpp.

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

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