NonlinearElasticityAssembler< DIM > Class Template Reference

#include <NonlinearElasticityAssembler.hpp>

Inherits AbstractNonlinearElasticityAssembler< DIM >.

Inherited by AbstractCardiacMechanicsAssembler< DIM >.

Collaboration diagram for NonlinearElasticityAssembler< DIM >:

Public Member Functions
	NonlinearElasticityAssembler (QuadraticMesh< DIM > pQuadMesh, AbstractIncompressibleMaterialLaw< DIM > pMaterialLaw, c_vector< double, DIM > bodyForce, double density, std::string outputDirectory, std::vector< unsigned > &fixedNodes, std::vector< c_vector< double, DIM > > *pFixedNodeLocations=NULL)
	NonlinearElasticityAssembler (QuadraticMesh< DIM > pQuadMesh, std::vector< AbstractIncompressibleMaterialLaw< DIM > > &rMaterialLaws, c_vector< double, DIM > bodyForce, double density, std::string outputDirectory, std::vector< unsigned > &fixedNodes, std::vector< c_vector< double, DIM > > *pFixedNodeLocations=NULL)
	~NonlinearElasticityAssembler ()
void	SetSurfaceTractionBoundaryConditions (std::vector< BoundaryElement< DIM-1, DIM > * > &rBoundaryElements, std::vector< c_vector< double, DIM > > &rSurfaceTractions)
void	SetFunctionalTractionBoundaryCondition (std::vector< BoundaryElement< DIM-1, DIM > * > rBoundaryElements, c_vector< double, DIM >(*pFunction)(c_vector< double, DIM > &))
std::vector< double > &	rGetPressures ()
std::vector< c_vector< double, DIM > > &	rGetDeformedPosition ()
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)
virtual void	AssembleOnBoundaryElement (BoundaryElement< DIM-1, DIM > &rBoundaryElement, c_matrix< double, BOUNDARY_STENCIL_SIZE, BOUNDARY_STENCIL_SIZE > &rAelem, c_vector< double, BOUNDARY_STENCIL_SIZE > &rBelem, c_vector< double, DIM > &rTraction, bool assembleResidual, bool assembleJacobian)
void	FormInitialGuess ()
void	AssembleSystem (bool assembleResidual, bool assembleJacobian)
void	Initialise (std::vector< c_vector< double, DIM > > *pFixedNodeLocations)
void	AllocateMatrixMemory ()
Protected Attributes
QuadraticMesh< DIM > *	mpQuadMesh
std::vector< BoundaryElement < DIM-1, DIM > * >	mBoundaryElements
GaussianQuadratureRule< DIM > *	mpQuadratureRule
GaussianQuadratureRule< DIM-1 > *	mpBoundaryQuadratureRule
Static Protected Attributes
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	STENCIL_SIZE = DIM*NUM_NODES_PER_ELEMENT + NUM_VERTICES_PER_ELEMENT
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 + DIM
Friends
class	TestNonlinearElasticityAssembler

Detailed Description

template<size_t DIM>
class NonlinearElasticityAssembler< DIM >

Todo:: : factor out Dof handling?

Finite elasticity assembler. Solves static incompressible nonlinear elasticity problems with arbitrary material laws and a body force.

Uses quadratic-linear bases (for displacement and pressure), and is therefore outside the assembler hierachy.

Currently only works with fixed nodes BCs (ie zerodisplacement) and zero-surface tractions on the rest of the boundary.

Definition at line 61 of file NonlinearElasticityAssembler.hpp.

Constructor & Destructor Documentation

template<size_t DIM>

NonlinearElasticityAssembler< DIM >::NonlinearElasticityAssembler	(	QuadraticMesh< DIM > *	pQuadMesh,
		AbstractIncompressibleMaterialLaw< DIM > *	pMaterialLaw,
		c_vector< double, DIM >	bodyForce,
		double	density,
		std::string	outputDirectory,
		std::vector< unsigned > &	fixedNodes,
		std::vector< c_vector< double, DIM > > *	pFixedNodeLocations = `NULL`
	)			`[inline]`

Constructor taking in mesh, material law (assuming homogeniety at the moment) body force, density, the fixed nodes (all the fixed nodes, including non-vertices), and the output directory.

Parameters:

	pQuadMesh
	pMaterialLaw
	bodyForce
	density
	outputDirectory
	fixedNodes
	pFixedNodeLocations	(defaults to NULL)

Definition at line 737 of file NonlinearElasticityAssembler.cpp.

References NonlinearElasticityAssembler< DIM >::Initialise().

template<size_t DIM>

NonlinearElasticityAssembler< DIM >::NonlinearElasticityAssembler	(	QuadraticMesh< DIM > *	pQuadMesh,
		std::vector< AbstractIncompressibleMaterialLaw< DIM > * > &	rMaterialLaws,
		c_vector< double, DIM >	bodyForce,
		double	density,
		std::string	outputDirectory,
		std::vector< unsigned > &	fixedNodes,
		std::vector< c_vector< double, DIM > > *	pFixedNodeLocations = `NULL`
	)			`[inline]`

Variant constructor taking a vector of material laws.

Parameters:

	pQuadMesh
	rMaterialLaws
	bodyForce
	density
	outputDirectory
	fixedNodes
	pFixedNodeLocations	(defaults to NULL)

Definition at line 755 of file NonlinearElasticityAssembler.cpp.

References AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetNumElements(), and NonlinearElasticityAssembler< DIM >::Initialise().

template<size_t DIM>

NonlinearElasticityAssembler< DIM >::~NonlinearElasticityAssembler ( ) [inline]

Destructor frees memory for quadrature rules.

Definition at line 774 of file NonlinearElasticityAssembler.cpp.

References NonlinearElasticityAssembler< DIM >::mpBoundaryQuadratureRule, and NonlinearElasticityAssembler< DIM >::mpQuadratureRule.

Member Function Documentation

template<size_t DIM>

void NonlinearElasticityAssembler< DIM >::AllocateMatrixMemory ( ) [inline, protected]

Allocates memory for the Jacobian and preconditioner matrices (larger number of non-zeros per row than with say linear problems)

Definition at line 646 of file NonlinearElasticityAssembler.cpp.

References PetscTools::GetNumProcs(), LinearSystem::GetOwnershipRange(), AbstractNonlinearElasticityAssembler< DIM >::mNumDofs, AbstractNonlinearElasticityAssembler< DIM >::mpLinearSystem, AbstractNonlinearElasticityAssembler< DIM >::mpPreconditionMatrixLinearSystem, NonlinearElasticityAssembler< DIM >::mpQuadMesh, and LinearSystem::rGetLhsMatrix().

Referenced by NonlinearElasticityAssembler< DIM >::Initialise().

template<size_t DIM>

void NonlinearElasticityAssembler< DIM >::AssembleOnBoundaryElement	(	BoundaryElement< DIM-1, DIM > &	rBoundaryElement,
		c_matrix< double, BOUNDARY_STENCIL_SIZE, BOUNDARY_STENCIL_SIZE > &	rAelem,
		c_vector< double, BOUNDARY_STENCIL_SIZE > &	rBelem,
		c_vector< double, DIM > &	rTraction,
		bool	assembleResidual,
		bool	assembleJacobian
	)			`[inline, protected, virtual]`

Compute the term from the surface integral of s*phi, where s is a specified non-zero surface traction (ie Neumann boundary condition) to be added to the Rhs vector.

Parameters:

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

Definition at line 514 of file NonlinearElasticityAssembler.cpp.

References AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetIndex(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNodeGlobalIndex(), GaussianQuadratureRule< ELEMENT_DIM >::GetNumQuadPoints(), GaussianQuadratureRule< ELEMENT_DIM >::GetWeight(), NonlinearElasticityAssembler< DIM >::mpBoundaryQuadratureRule, NonlinearElasticityAssembler< DIM >::mpQuadMesh, AbstractNonlinearElasticityAssembler< DIM >::mpTractionBoundaryConditionFunction, AbstractNonlinearElasticityAssembler< DIM >::mUsingTractionBoundaryConditionFunction, NonlinearElasticityAssembler< DIM >::NUM_NODES_PER_BOUNDARY_ELEMENT, and GaussianQuadratureRule< ELEMENT_DIM >::rGetQuadPoint().

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

template<size_t DIM>

void NonlinearElasticityAssembler< 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
	)			`[inline, protected, virtual]`

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].

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.

Reimplemented in AbstractCardiacMechanicsAssembler< DIM >.

Definition at line 191 of file NonlinearElasticityAssembler.cpp.

References AbstractIncompressibleMaterialLaw< DIM >::ComputeStressAndStressDerivative(), AbstractNonlinearElasticityAssembler< DIM >::dTdE, AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetIndex(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNodeGlobalIndex(), GaussianQuadratureRule< ELEMENT_DIM >::GetNumQuadPoints(), GaussianQuadratureRule< ELEMENT_DIM >::GetWeight(), AbstractNonlinearElasticityAssembler< DIM >::mBodyForce, AbstractNonlinearElasticityAssembler< DIM >::mCurrentSolution, AbstractNonlinearElasticityAssembler< DIM >::mDensity, AbstractNonlinearElasticityAssembler< DIM >::mMaterialLaws, AbstractNonlinearElasticityAssembler< DIM >::mpBodyForceFunction, NonlinearElasticityAssembler< DIM >::mpQuadMesh, NonlinearElasticityAssembler< DIM >::mpQuadratureRule, AbstractNonlinearElasticityAssembler< DIM >::mUsingBodyForceFunction, NonlinearElasticityAssembler< DIM >::NUM_NODES_PER_ELEMENT, NonlinearElasticityAssembler< DIM >::NUM_VERTICES_PER_ELEMENT, GaussianQuadratureRule< ELEMENT_DIM >::rGetQuadPoint(), FourthOrderTensor< DIM >::SetAsProduct(), and NonlinearElasticityAssembler< DIM >::STENCIL_SIZE.

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

template<size_t DIM>

void NonlinearElasticityAssembler< DIM >::AssembleSystem	(	bool	assembleResidual,
		bool	assembleJacobian
	)			`[inline, protected, virtual]`

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 AbstractNonlinearElasticityAssembler< DIM >.

Definition at line 47 of file NonlinearElasticityAssembler.cpp.

Referenced by ImplicitCardiacMechanicsAssembler< DIM >::Solve(), and ExplicitCardiacMechanicsAssembler< DIM >::Solve().

template<size_t DIM>

void NonlinearElasticityAssembler< DIM >::FormInitialGuess ( ) [inline, protected, virtual]

Set up the current guess to be the solution given no displacement. The current solution (in 2d) is order as [u1 v1 u2 v2 ... uN vN p1 p2 .. pM] (where there are N total nodes and M vertices) so the initial guess is [0 0 0 0 ... 0 0 p1 p2 .. pM] where p_i are such that T is zero (depends on material law).

In a homogeneous problem, all p_i 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.

Implements AbstractNonlinearElasticityAssembler< DIM >.

Definition at line 578 of file NonlinearElasticityAssembler.cpp.

References AbstractNonlinearElasticityAssembler< DIM >::mCurrentSolution, AbstractNonlinearElasticityAssembler< DIM >::mMaterialLaws, AbstractNonlinearElasticityAssembler< DIM >::mNumDofs, NonlinearElasticityAssembler< DIM >::mpQuadMesh, and NonlinearElasticityAssembler< DIM >::NUM_VERTICES_PER_ELEMENT.

Referenced by NonlinearElasticityAssembler< DIM >::Initialise().

template<size_t DIM>

void NonlinearElasticityAssembler< DIM >::Initialise ( std::vector< c_vector< double, DIM > > * pFixedNodeLocations ) [inline, protected]

Initialise the assembler.

Parameters:

pFixedNodeLocations

Definition at line 606 of file NonlinearElasticityAssembler.cpp.

References NonlinearElasticityAssembler< DIM >::AllocateMatrixMemory(), NonlinearElasticityAssembler< DIM >::FormInitialGuess(), AbstractNonlinearElasticityAssembler< DIM >::mFixedNodeDisplacements, AbstractNonlinearElasticityAssembler< DIM >::mFixedNodes, NonlinearElasticityAssembler< DIM >::mpBoundaryQuadratureRule, NonlinearElasticityAssembler< DIM >::mpQuadMesh, and NonlinearElasticityAssembler< DIM >::mpQuadratureRule.

Referenced by NonlinearElasticityAssembler< DIM >::NonlinearElasticityAssembler().

template<size_t DIM>

std::vector< c_vector< double, DIM > > & NonlinearElasticityAssembler< DIM >::rGetDeformedPosition ( ) [inline, virtual]

Get the deformed position. Note returnvalue[i](j) = x_j for node i.

Implements AbstractNonlinearElasticityAssembler< DIM >.

Definition at line 814 of file NonlinearElasticityAssembler.cpp.

References AbstractNonlinearElasticityAssembler< DIM >::mCurrentSolution, AbstractNonlinearElasticityAssembler< DIM >::mDeformedPosition, and NonlinearElasticityAssembler< DIM >::mpQuadMesh.

template<size_t DIM>

std::vector< double > & NonlinearElasticityAssembler< DIM >::rGetPressures ( ) [inline]

Get pressures.

Definition at line 801 of file NonlinearElasticityAssembler.cpp.

References AbstractNonlinearElasticityAssembler< DIM >::mCurrentSolution, NonlinearElasticityAssembler< DIM >::mpQuadMesh, and AbstractNonlinearElasticityAssembler< DIM >::mPressures.

template<size_t DIM>

void NonlinearElasticityAssembler< DIM >::SetFunctionalTractionBoundaryCondition	(	std::vector< BoundaryElement< DIM-1, DIM > * >	rBoundaryElements,
		c_vector< double, DIM >(*)(c_vector< double, DIM > &)	pFunction
	)			`[inline]`

Set a function which gives the surface traction as a function of X (undeformed position), together with the surface elements which make up the Neumann part of the boundary.

Parameters:

	rBoundaryElements
	pFunction

Definition at line 791 of file NonlinearElasticityAssembler.cpp.

References NonlinearElasticityAssembler< DIM >::mBoundaryElements, AbstractNonlinearElasticityAssembler< DIM >::mpTractionBoundaryConditionFunction, and AbstractNonlinearElasticityAssembler< DIM >::mUsingTractionBoundaryConditionFunction.

template<size_t DIM>

void NonlinearElasticityAssembler< DIM >::SetSurfaceTractionBoundaryConditions	(	std::vector< BoundaryElement< DIM-1, DIM > * > &	rBoundaryElements,
		std::vector< c_vector< double, DIM > > &	rSurfaceTractions
	)			`[inline]`

Specify traction boundary conditions (if this is not called zero surface tractions are assumed. This method takes in a list of boundary elements and a corresponding list of surface tractions.

Parameters: