#include <IncompressibleNonlinearElasticitySolver.hpp>

Inheritance diagram for IncompressibleNonlinearElasticitySolver< DIM >:

Collaboration diagram for IncompressibleNonlinearElasticitySolver< DIM >:

Public Member Functions
	IncompressibleNonlinearElasticitySolver (AbstractTetrahedralMesh< DIM, DIM > &rQuadMesh, SolidMechanicsProblemDefinition< DIM > &rProblemDefinition, std::string outputDirectory)

virtual	~IncompressibleNonlinearElasticitySolver ()

Public Member Functions inherited from AbstractNonlinearElasticitySolver< DIM >
void	ComputeResidual (Vec currentGuess, Vec residualVector)

void	ComputeJacobian (Vec currentGuess, Mat pJacobian, Mat pPreconditioner)

	AbstractNonlinearElasticitySolver (AbstractTetrahedralMesh< DIM, DIM > &rQuadMesh, SolidMechanicsProblemDefinition< DIM > &rProblemDefinition, std::string outputDirectory, CompressibilityType compressibilityType)

virtual	~AbstractNonlinearElasticitySolver ()

void	Solve (double tol=-1.0)

void	SetIncludeActiveTension (bool includeActiveTension=true)

unsigned	GetNumNewtonIterations ()

void	SetWriteOutputEachNewtonIteration (bool writeOutputEachNewtonIteration=true)

void	SetKspAbsoluteTolerance (double kspAbsoluteTolerance)

void	SetTakeFullFirstNewtonStep (bool takeFullFirstStep=true)

void	SetUsePetscDirectSolve (bool usePetscDirectSolve=true)

void	SetCurrentTime (double time)

void	CreateCmguiOutput ()

void	WriteCurrentStrains (StrainType strainType, std::string fileName, int counterToAppend=-1)

void	SetComputeAverageStressPerElementDuringSolve (bool setComputeAverageStressPerElement=true)

void	WriteCurrentAverageElementStresses (std::string fileName, int counterToAppend=-1)

std::vector< c_vector< double, DIM > > &	rGetSpatialSolution ()

std::vector< c_vector< double, DIM > > &	rGetDeformedPosition ()

c_matrix< double, DIM, DIM >	GetAverageStressPerElement (unsigned elementIndex)

Public Member Functions inherited from AbstractContinuumMechanicsSolver< DIM >
	AbstractContinuumMechanicsSolver (AbstractTetrahedralMesh< DIM, DIM > &rQuadMesh, ContinuumMechanicsProblemDefinition< DIM > &rProblemDefinition, std::string outputDirectory, CompressibilityType compressibilityType)

virtual	~AbstractContinuumMechanicsSolver ()

void	WriteCurrentSpatialSolution (std::string fileName, std::string fileExtension, int counterToAppend=-1)

void	WriteCurrentPressureSolution (int counterToAppend=-1)

void	SetWriteOutput (bool writeOutput=true)

void	CreateVtkOutput (std::string spatialSolutionName="Spatial solution")

std::vector< double > &	rGetCurrentSolution ()

std::vector< double > &	rGetPressures ()

Protected Member Functions
virtual void	AssembleOnElement (Element< DIM, DIM > &rElement, c_matrix< double, STENCIL_SIZE, STENCIL_SIZE > &rAElem, c_matrix< double, STENCIL_SIZE, STENCIL_SIZE > &rAElemPrecond, c_vector< double, STENCIL_SIZE > &rBElem, bool assembleResidual, bool assembleJacobian)

void	FormInitialGuess ()

void	AssembleSystem (bool assembleResidual, bool assembleJacobian)

Protected Member Functions inherited from AbstractNonlinearElasticitySolver< DIM >
void	AddStressToAverageStressPerElement (c_matrix< double, DIM, DIM > &rT, unsigned elementIndex)

virtual void	SetKspSolverAndPcType (KSP solver)

virtual void	FinishAssembleSystem (bool assembleResidual, bool assembleLinearSystem)

void	GetElementCentroidStrain (StrainType strainType, Element< DIM, DIM > &rElement, c_matrix< double, DIM, DIM > &rDeformationGradient)

virtual void	AddActiveStressAndStressDerivative (c_matrix< double, DIM, DIM > &rC, unsigned elementIndex, unsigned currentQuadPointGlobalIndex, c_matrix< double, DIM, DIM > &rT, FourthOrderTensor< DIM, DIM, DIM, DIM > &rDTdE, bool addToDTdE)

virtual void	SetupChangeOfBasisMatrix (unsigned elementIndex, unsigned currentQuadPointGlobalIndex)

void	AssembleOnBoundaryElement (BoundaryElement< DIM-1, DIM > &rBoundaryElement, c_matrix< double, BOUNDARY_STENCIL_SIZE, BOUNDARY_STENCIL_SIZE > &rAelem, c_vector< double, BOUNDARY_STENCIL_SIZE > &rBelem, bool assembleResidual, bool assembleJacobian, unsigned boundaryConditionIndex)

bool	ShouldAssembleMatrixTermForPressureOnDeformedBc ()

void	AssembleOnBoundaryElementForPressureOnDeformedBc (BoundaryElement< DIM-1, DIM > &rBoundaryElement, c_matrix< double, BOUNDARY_STENCIL_SIZE, BOUNDARY_STENCIL_SIZE > &rAelem, c_vector< double, BOUNDARY_STENCIL_SIZE > &rBelem, bool assembleResidual, bool assembleJacobian, unsigned boundaryConditionIndex)

double	ComputeResidualAndGetNorm (bool allowException)

double	CalculateResidualNorm ()

void	VectorSum (std::vector< double > &rX, ReplicatableVector &rY, double a, std::vector< double > &rZ)

void	PrintLineSearchResult (double s, double residNorm)

double	TakeNewtonStep ()

double	UpdateSolutionUsingLineSearch (Vec solution)

virtual void	PostNewtonStep (unsigned counter, double normResidual)

void	SolveNonSnes (double tol=-1.0)

Protected Member Functions inherited from AbstractContinuumMechanicsSolver< DIM >
void	AllocateMatrixMemory ()

void	ApplyDirichletBoundaryConditions (ApplyDirichletBcsType type, bool symmetricProblem)

void	AddIdentityBlockForDummyPressureVariables (ApplyDirichletBcsType type)

void	RemovePressureDummyValuesThroughLinearInterpolation ()

Static Protected Attributes
static const size_t	NUM_NODES_PER_ELEMENT = AbstractNonlinearElasticitySolver<DIM>::NUM_NODES_PER_ELEMENT

static const size_t	NUM_VERTICES_PER_ELEMENT = AbstractNonlinearElasticitySolver<DIM>::NUM_VERTICES_PER_ELEMENT

static const size_t	NUM_NODES_PER_BOUNDARY_ELEMENT = AbstractNonlinearElasticitySolver<DIM>::NUM_NODES_PER_BOUNDARY_ELEMENT

static const size_t	STENCIL_SIZE = DIM*NUM_NODES_PER_ELEMENT + NUM_VERTICES_PER_ELEMENT

static const size_t	BOUNDARY_STENCIL_SIZE = DIM*NUM_NODES_PER_BOUNDARY_ELEMENT

Static Protected Attributes inherited from AbstractNonlinearElasticitySolver< DIM >
static const size_t	NUM_VERTICES_PER_ELEMENT = DIM+1

static const size_t	NUM_NODES_PER_ELEMENT = (DIM+1)*(DIM+2)/2

static const size_t	NUM_NODES_PER_BOUNDARY_ELEMENT = DIM*(DIM+1)/2

static const size_t	BOUNDARY_STENCIL_SIZE = DIM*NUM_NODES_PER_BOUNDARY_ELEMENT

static double	MAX_NEWTON_ABS_TOL = 1e-7

static double	MIN_NEWTON_ABS_TOL = 1e-10

static double	NEWTON_REL_TOL = 1e-4

Friends
class	TestIncompressibleNonlinearElasticitySolver

class	TestCompressibleNonlinearElasticitySolver

class	TestNonlinearElasticityAdjointSolver

class	AdaptiveNonlinearElasticityProblem

Additional Inherited Members
Protected Attributes inherited from AbstractNonlinearElasticitySolver< DIM >
SolidMechanicsProblemDefinition < DIM > &	mrProblemDefinition

Mat &	mrJacobianMatrix

c_matrix< double, DIM, DIM >	mChangeOfBasisMatrix

double	mKspAbsoluteTol

bool	mWriteOutputEachNewtonIteration

FourthOrderTensor< DIM, DIM, DIM, DIM >	dTdE

unsigned	mNumNewtonIterations

double	mCurrentTime

bool	mCheckedOutwardNormals

bool	mUseSnesSolver

double	mLastDampingValue

bool	mFirstStep

bool	mTakeFullFirstNewtonStep

bool	mPetscDirectSolve

bool	mIncludeActiveTension

bool	mSetComputeAverageStressPerElement

std::vector< c_vector< double, DIM *(DIM+1)/2 > >	mAverageStressesPerElement

Protected Attributes inherited from AbstractContinuumMechanicsSolver< DIM >
AbstractTetrahedralMesh< DIM, DIM > &	mrQuadMesh

ContinuumMechanicsProblemDefinition < DIM > &	mrProblemDefinition

bool	mWriteOutput

std::string	mOutputDirectory

OutputFileHandler *	mpOutputFileHandler

std::vector< c_vector< double, DIM > >	mSpatialSolution

std::vector< double >	mPressureSolution

std::vector< double >	mCurrentSolution

GaussianQuadratureRule< DIM > *	mpQuadratureRule

GaussianQuadratureRule< DIM-1 > *	mpBoundaryQuadratureRule

CompressibilityType	mCompressibilityType

unsigned	mProblemDimension

unsigned	mNumDofs

bool	mVerbose

Vec	mResidualVector

Vec	mLinearSystemRhsVector

Mat	mSystemLhsMatrix

Vec	mDirichletBoundaryConditionsVector

Mat	mPreconditionMatrix

Detailed Description

template<size_t DIM>
class IncompressibleNonlinearElasticitySolver< DIM >

Finite elasticity solver. Solves static *incompressible* nonlinear elasticity problems with arbitrary (incompressible) material laws and a body force.

Uses quadratic-linear bases (for displacement and pressure), and is therefore outside other assembler or solver hierarchy.

Definition at line 60 of file IncompressibleNonlinearElasticitySolver.hpp.

Constructor & Destructor Documentation

template<size_t DIM>

IncompressibleNonlinearElasticitySolver< DIM >::IncompressibleNonlinearElasticitySolver	(	AbstractTetrahedralMesh< DIM, DIM > &	rQuadMesh,
		SolidMechanicsProblemDefinition< DIM > &	rProblemDefinition,
		std::string	outputDirectory
	)

Constructor.

Parameters

rQuadMesh	The quadratic mesh to solve on
rProblemDefinition	an object defining in particular the body force and boundary conditions
outputDirectory	The output directory

Definition at line 621 of file IncompressibleNonlinearElasticitySolver.cpp.

References EXCEPTION, IncompressibleNonlinearElasticitySolver< DIM >::FormInitialGuess(), and SolidMechanicsProblemDefinition< DIM >::GetCompressibilityType().

template<size_t DIM>

virtual IncompressibleNonlinearElasticitySolver< DIM >::~IncompressibleNonlinearElasticitySolver ( )

inlinevirtual

Destructor.

Definition at line 155 of file IncompressibleNonlinearElasticitySolver.hpp.

Member Function Documentation

template<size_t DIM>

void IncompressibleNonlinearElasticitySolver< DIM >::AssembleOnElement	(	Element< DIM, DIM > &	rElement,
		c_matrix< double, STENCIL_SIZE, STENCIL_SIZE > &	rAElem,
		c_matrix< double, STENCIL_SIZE, STENCIL_SIZE > &	rAElemPrecond,
		c_vector< double, STENCIL_SIZE > &	rBElem,
		bool	assembleResidual,
		bool	assembleJacobian
	)

protectedvirtual

Assemble residual or Jacobian on an element, using the current solution stored in mCurrrentSolution. The ordering assumed is (in 2d) rBElem = [u0 v0 u1 v1 .. u5 v5 p0 p1 p2]. (This ordering in used at the element level, but not in the global matrix/vector).

Parameters

rElement	The element to assemble on.
rAElem	The element's contribution to the LHS matrix is returned in this n by n matrix, where n is the no. of nodes in this element. There is no need to zero this matrix before calling.
rAElemPrecond	The element's contribution to the matrix passed to PetSC in creating a preconditioner
rBElem	The element's contribution to the RHS vector is returned in this vector of length n, the no. of nodes in this element. There is no need to zero this vector before calling.
assembleResidual	A bool stating whether to assemble the residual vector.
assembleJacobian	A bool stating whether to assemble the Jacobian matrix.

Definition at line 210 of file IncompressibleNonlinearElasticitySolver.cpp.

References QuadraticBasisFunction< ELEMENT_DIM >::ComputeBasisFunctions(), LinearBasisFunction< ELEMENT_DIM >::ComputeBasisFunctions(), AbstractMaterialLaw< DIM >::ComputeStressAndStressDerivative(), QuadraticBasisFunction< ELEMENT_DIM >::ComputeTransformedBasisFunctionDerivatives(), Determinant(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetIndex(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNodeGlobalIndex(), Inverse(), NEVER_REACHED, and AbstractMaterialLaw< DIM >::SetChangeOfBasisMatrix().

template<size_t DIM>

void IncompressibleNonlinearElasticitySolver< DIM >::AssembleSystem	(	bool	assembleResidual,
		bool	assembleJacobian
	)

protectedvirtual

Assemble the residual vector (using the current solution stored in mCurrentSolution, output going to mpLinearSystem->rGetRhsVector), or Jacobian matrix (using the current solution stored in mCurrentSolution, output going to mpLinearSystem->rGetLhsMatrix).

Parameters

assembleResidual	A bool stating whether to assemble the residual vector.
assembleJacobian	A bool stating whether to assemble the Jacobian matrix.

Implements AbstractNonlinearElasticitySolver< DIM >.

Definition at line 52 of file IncompressibleNonlinearElasticitySolver.cpp.

References PetscVecTools::Finalise(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetElementIteratorBegin(), PetscTools::GetMyRank(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNodeGlobalIndex(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetOwnership(), CommandLineArguments::Instance(), CommandLineArguments::OptionExists(), PetscMatTools::SwitchWriteMode(), PetscVecTools::Zero(), and PetscMatTools::Zero().

template<size_t DIM>

void IncompressibleNonlinearElasticitySolver< DIM >::FormInitialGuess ( )

protected

Set up the current guess to be the solution given no displacement.

The initial guess is zero for spatial variables, 0 for dummy pressure variables, and the appropriate choice of pressure such that the initial stress is zero (depends on material law)

In a homogeneous problem, all (the non-dummy) pressures are the same. In a heterogeneous problem, p for a given vertex is the zero-strain-pressure for ONE of the elements containing that vertex (which element containing the vertex is reached LAST). In this case the initial guess will be close but not exactly the solution given zero body force.