#include <AbstractNonlinearAssemblerSolverHybrid.hpp>

Inheritance diagram for AbstractNonlinearAssemblerSolverHybrid< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >:

Collaboration diagram for AbstractNonlinearAssemblerSolverHybrid< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >:

Public Member Functions
void	ComputeResidual (const Vec currentGuess, Vec residualVector)

void	ComputeJacobian (const Vec currentGuess, Mat *pJacobian)

	AbstractNonlinearAssemblerSolverHybrid (AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > pMesh, BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM > pBoundaryConditions)

virtual	~AbstractNonlinearAssemblerSolverHybrid ()

virtual Vec	Solve (Vec initialGuess, bool useAnalyticalJacobian=false)

void	SetNonlinearSolver (AbstractNonlinearSolver *pNonlinearSolver)

bool	VerifyJacobian (double tol)

Public Member Functions inherited from AbstractFeVolumeIntegralAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, true, true, NONLINEAR >
	AbstractFeVolumeIntegralAssembler (AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *pMesh)

virtual	~AbstractFeVolumeIntegralAssembler ()

Public Member Functions inherited from AbstractFeAssemblerCommon< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX, INTERPOLATION_LEVEL >
	AbstractFeAssemblerCommon ()

void	SetCurrentSolution (Vec currentSolution)

virtual	~AbstractFeAssemblerCommon ()

Public Member Functions inherited from AbstractFeAssemblerInterface< CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX >
	AbstractFeAssemblerInterface ()

void	SetMatrixToAssemble (Mat &rMatToAssemble, bool zeroMatrixBeforeAssembly=true)

void	SetVectorToAssemble (Vec &rVecToAssemble, bool zeroVectorBeforeAssembly)

void	Assemble ()

void	AssembleMatrix ()

void	AssembleVector ()

virtual	~AbstractFeAssemblerInterface ()

Protected Member Functions
void	ApplyDirichletConditions (Vec currentGuess, Vec residual, Mat *pMat)

void	ComputeJacobianNumerically (const Vec currentGuess, Mat *pJacobian)

Protected Member Functions inherited from AbstractFeVolumeIntegralAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, true, true, NONLINEAR >
void	ComputeTransformedBasisFunctionDerivatives (const ChastePoint< ELEMENT_DIM > &rPoint, const c_matrix< double, ELEMENT_DIM, SPACE_DIM > &rInverseJacobian, c_matrix< double, SPACE_DIM, ELEMENT_DIM+1 > &rReturnValue)

void	DoAssemble ()

virtual c_matrix< double, PROBLEM_DIM (ELEMENT_DIM+1), PROBLEM_DIM (ELEMENT_DIM+1)>	ComputeMatrixTerm (c_vector< double, ELEMENT_DIM+1 > &rPhi, c_matrix< double, SPACE_DIM, ELEMENT_DIM+1 > &rGradPhi, ChastePoint< SPACE_DIM > &rX, c_vector< double, PROBLEM_DIM > &rU, c_matrix< double, PROBLEM_DIM, SPACE_DIM > &rGradU, Element< ELEMENT_DIM, SPACE_DIM > *pElement)

virtual c_vector< double, PROBLEM_DIM *(ELEMENT_DIM+1)>	ComputeVectorTerm (c_vector< double, ELEMENT_DIM+1 > &rPhi, c_matrix< double, SPACE_DIM, ELEMENT_DIM+1 > &rGradPhi, ChastePoint< SPACE_DIM > &rX, c_vector< double, PROBLEM_DIM > &rU, c_matrix< double, PROBLEM_DIM, SPACE_DIM > &rGradU, Element< ELEMENT_DIM, SPACE_DIM > *pElement)

virtual void	AssembleOnElement (Element< ELEMENT_DIM, SPACE_DIM > &rElement, c_matrix< double, PROBLEM_DIM (ELEMENT_DIM+1), PROBLEM_DIM (ELEMENT_DIM+1) > &rAElem, c_vector< double, PROBLEM_DIM *(ELEMENT_DIM+1)> &rBElem)

virtual bool	ElementAssemblyCriterion (Element< ELEMENT_DIM, SPACE_DIM > &rElement)

Protected Member Functions inherited from AbstractFeAssemblerCommon< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX, INTERPOLATION_LEVEL >
virtual double	GetCurrentSolutionOrGuessValue (unsigned nodeIndex, unsigned indexOfUnknown)

virtual void	ResetInterpolatedQuantities ()

virtual void	IncrementInterpolatedQuantities (double phiI, const Node< SPACE_DIM > *pNode)

virtual void	IncrementInterpolatedGradientQuantities (const c_matrix< double, SPACE_DIM, ELEMENT_DIM+1 > &rGradPhi, unsigned phiIndex, const Node< SPACE_DIM > *pNode)

Protected Attributes
AbstractTetrahedralMesh < ELEMENT_DIM, SPACE_DIM > *	mpMesh

BoundaryConditionsContainer < ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM > *	mpBoundaryConditions

AbstractNonlinearSolver *	mpSolver

bool	mWeAllocatedSolverMemory

bool	mUseAnalyticalJacobian

NaturalNeumannSurfaceTermAssembler < ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM > *	mpNeumannSurfaceTermsAssembler

Protected Attributes inherited from AbstractFeVolumeIntegralAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, true, true, NONLINEAR >
AbstractTetrahedralMesh < ELEMENT_DIM, SPACE_DIM > *	mpMesh

GaussianQuadratureRule < ELEMENT_DIM > *	mpQuadRule

Protected Attributes inherited from AbstractFeAssemblerCommon< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX, INTERPOLATION_LEVEL >
ReplicatableVector	mCurrentSolutionOrGuessReplicated

Protected Attributes inherited from AbstractFeAssemblerInterface< CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX >
Vec	mVectorToAssemble

Mat	mMatrixToAssemble

bool	mAssembleMatrix

bool	mAssembleVector

bool	mZeroMatrixBeforeAssembly

bool	mZeroVectorBeforeAssembly

PetscInt	mOwnershipRangeLo

PetscInt	mOwnershipRangeHi

Additional Inherited Members
Protected Types inherited from AbstractFeVolumeIntegralAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, true, true, NONLINEAR >
typedef LinearBasisFunction < ELEMENT_DIM >	BasisFunction

Detailed Description

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
class AbstractNonlinearAssemblerSolverHybrid< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >

The ASSEMBLER-SOLVER class.

An abstract solver for solving nonlinear elliptic PDEs.

Definition at line 132 of file AbstractNonlinearAssemblerSolverHybrid.hpp.

Constructor & Destructor Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

AbstractNonlinearAssemblerSolverHybrid< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::AbstractNonlinearAssemblerSolverHybrid	(	AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *	pMesh,
		BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM > *	pBoundaryConditions
	)

Constructor.

Parameters

pMesh	The mesh
pBoundaryConditions	The boundary conditions to apply

Definition at line 251 of file AbstractNonlinearAssemblerSolverHybrid.hpp.

References AbstractNonlinearAssemblerSolverHybrid< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpMesh, AbstractNonlinearAssemblerSolverHybrid< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpNeumannSurfaceTermsAssembler, AbstractNonlinearAssemblerSolverHybrid< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpSolver, and AbstractNonlinearAssemblerSolverHybrid< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mWeAllocatedSolverMemory.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

AbstractNonlinearAssemblerSolverHybrid< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::~AbstractNonlinearAssemblerSolverHybrid ( )

virtual

Destructor.

Definition at line 275 of file AbstractNonlinearAssemblerSolverHybrid.hpp.

Member Function Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

void AbstractNonlinearAssemblerSolverHybrid< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::ApplyDirichletConditions	(	Vec	currentGuess,
		Vec	residual,
		Mat *	pMat
	)

protected

Apply Dirichlet boundary conditions to either the residual or Jacobian.

Parameters

currentGuess	the solution guess for the current nonlinear solver iteration
residual	the residual to apply boundary conditions to (can be NULL if bcs to be applied to Jacobian only)
pMat	the Jacobian to apply boundary conditions to (can be NULL if bcs to be applied to residual only)

Definition at line 285 of file AbstractNonlinearAssemblerSolverHybrid.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

void AbstractNonlinearAssemblerSolverHybrid< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::ComputeJacobian	(	const Vec	currentGuess,
		Mat *	pJacobian
	)

Compute the Jacobian matrix given a current guess at the solution. Choose whether to use a numerical or analytical method based on a flag provided by the user (in Solve()).

Parameters

currentGuess	The solution guess for the current iteration.
pJacobian	Pointer to object to fill with the Jacobian matrix.

NOTE: this method is called indirectly by the PETSc iterative solvers, so must be public.

Definition at line 321 of file AbstractNonlinearAssemblerSolverHybrid.hpp.

References PetscMatTools::Finalise(), and PetscMatTools::SwitchWriteMode().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

void AbstractNonlinearAssemblerSolverHybrid< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::ComputeJacobianNumerically	(	const Vec	currentGuess,
		Mat *	pJacobian
	)

protected

Computes the Jacobian numerically i.e. an approximation, using numerical partial derivatives.

Parameters

currentGuess	Independent variable, u in f(u), for example
pJacobian	A pointer to the Jacobian matrix

Todo:: This loop is setting the column "global_index_outer" of the Jacobian matrix to the result vector in a non-sparse way.

Definition at line 342 of file AbstractNonlinearAssemblerSolverHybrid.hpp.

References PetscVecTools::AddToElement(), PetscTools::CreateVec(), PetscTools::Destroy(), PetscMatTools::Finalise(), CompareDoubles::IsNearZero(), PetscVecTools::Scale(), PetscMatTools::SetElement(), and PetscVecTools::WAXPY().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

void AbstractNonlinearAssemblerSolverHybrid< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::ComputeResidual	(	const Vec	currentGuess,
		Vec	residualVector
	)

Compute the residual vector given the current solution guess.

Parameters

currentGuess	The solution guess for the current nonlinear solve iteration.
residualVector	We fill this with the residual vector.

NOTE: this method is called indirectly by the PETSc iterative solvers, so must be public.

Definition at line 300 of file AbstractNonlinearAssemblerSolverHybrid.hpp.

References PetscVecTools::Finalise().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

void AbstractNonlinearAssemblerSolverHybrid< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::SetNonlinearSolver ( AbstractNonlinearSolver * pNonlinearSolver )

SetNonlinearSolver - by default a SimplePetscNonlinearSolver is created and used in this class, this method can be called to use a different AbstractNonlinearSolver.

Parameters

pNonlinearSolver a nonlinear solver

Definition at line 432 of file AbstractNonlinearAssemblerSolverHybrid.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

Vec AbstractNonlinearAssemblerSolverHybrid< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::Solve	(	Vec	initialGuess,
		bool	useAnalyticalJacobian = `false`
	)

virtual

Assemble and solve the system for a nonlinear elliptic PDE.

Parameters

initialGuess	An initial guess for the iterative solver
useAnalyticalJacobian	Set to true to use an analytically calculated Jacobian matrix rather than a numerically approximated one.

Returns: A PETSc vector giving the solution at each mesh node.

Definition at line 408 of file AbstractNonlinearAssemblerSolverHybrid.hpp.

References EXCEPTION.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

bool AbstractNonlinearAssemblerSolverHybrid< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::VerifyJacobian ( double tol )

A helper method for use when writing concrete assemblers. Once the user has calculated (on paper) the weak form and the form of the ComputeMatrixTerm method, they can check whether the analytic Jacobian matches the numerical Jacobian to verify the correctness of the code.

Parameters

tol	A tolerance which defaults to 1e-5

Returns: true if the componentwise difference between the matrices is less than the tolerance, false otherwise.

This method should NOT be run in simulations - it is only to verify the correctness of the concrete assembler code. Allocates dense matrices.

Definition at line 443 of file AbstractNonlinearAssemblerSolverHybrid.hpp.

References PetscMatTools::CheckEquality(), PetscTools::CreateAndSetVec(), PetscTools::Destroy(), and PetscTools::SetupMat().

Member Data Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

BoundaryConditionsContainer<ELEMENT_DIM,SPACE_DIM,PROBLEM_DIM>* AbstractNonlinearAssemblerSolverHybrid< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpBoundaryConditions

protected

Boundary conditions container.

Definition at line 140 of file AbstractNonlinearAssemblerSolverHybrid.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

AbstractTetrahedralMesh<ELEMENT_DIM,SPACE_DIM>* AbstractNonlinearAssemblerSolverHybrid< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpMesh

protected

The mesh.

Definition at line 137 of file AbstractNonlinearAssemblerSolverHybrid.hpp.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

NaturalNeumannSurfaceTermAssembler<ELEMENT_DIM,SPACE_DIM,PROBLEM_DIM>* AbstractNonlinearAssemblerSolverHybrid< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpNeumannSurfaceTermsAssembler

protected

An assembler for the surface integral terms in the residual

Definition at line 152 of file AbstractNonlinearAssemblerSolverHybrid.hpp.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

AbstractNonlinearSolver* AbstractNonlinearAssemblerSolverHybrid< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpSolver

protected

The nonlinear solver.

Definition at line 143 of file AbstractNonlinearAssemblerSolverHybrid.hpp.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

bool AbstractNonlinearAssemblerSolverHybrid< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mUseAnalyticalJacobian

protected

Whether to use an analytical expression for the Jacobian.

Definition at line 149 of file AbstractNonlinearAssemblerSolverHybrid.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

bool AbstractNonlinearAssemblerSolverHybrid< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mWeAllocatedSolverMemory

protected

Whether memory has been allocated for the solver.

Definition at line 146 of file AbstractNonlinearAssemblerSolverHybrid.hpp.

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

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

pde/src/solver/AbstractNonlinearAssemblerSolverHybrid.hpp

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM> class AbstractNonlinearAssemblerSolverHybrid< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
class AbstractNonlinearAssemblerSolverHybrid< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >