#include <CellBasedPdeSolver.hpp>

Inheritance diagram for CellBasedPdeSolver< DIM >:

Collaboration diagram for CellBasedPdeSolver< DIM >:

Public Member Functions
	CellBasedPdeSolver (TetrahedralMesh< DIM, DIM > pMesh, AbstractLinearEllipticPde< DIM, DIM > pPde, BoundaryConditionsContainer< DIM, DIM, 1 > *pBoundaryConditions)

virtual	~CellBasedPdeSolver ()

Public Member Functions inherited from SimpleLinearEllipticSolver< DIM, DIM >
	SimpleLinearEllipticSolver (AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > pMesh, AbstractLinearEllipticPde< ELEMENT_DIM, SPACE_DIM > pPde, BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, 1 > *pBoundaryConditions)

void	InitialiseForSolve (Vec initialSolution=NULL)

Public Member Functions inherited from AbstractAssemblerSolverHybrid< ELEMENT_DIM, SPACE_DIM, 1, NORMAL >
	AbstractAssemblerSolverHybrid (AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > pMesh, BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM > pBoundaryConditions)

virtual	~AbstractAssemblerSolverHybrid ()

void	SetupGivenLinearSystem (Vec currentSolution, bool computeMatrix, LinearSystem *pLinearSystem)

Public Member Functions inherited from AbstractFeVolumeIntegralAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, true, true, INTERPOLATION_LEVEL >
	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 ()

Public Member Functions inherited from AbstractStaticLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, 1 >
	AbstractStaticLinearPdeSolver (AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *pMesh)

Vec	Solve (Vec initialGuess=NULL)

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

virtual	~AbstractLinearPdeSolver ()

virtual void	PrepareForSetupLinearSystem (Vec currentSolution)

virtual void	FinaliseLinearSystem (Vec currentSolution)

virtual void	FollowingSolveLinearSystem (Vec currentSolution)

LinearSystem *	GetLinearSystem ()

Protected Member Functions
virtual c_vector< double, 1 *(DIM+1)>	ComputeVectorTerm (c_vector< double, DIM+1 > &rPhi, c_matrix< double, DIM, DIM+1 > &rGradPhi, ChastePoint< DIM > &rX, c_vector< double, 1 > &rU, c_matrix< double, 1, DIM > &rGradU, Element< DIM, DIM > *pElement)

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

void	ResetInterpolatedQuantities ()

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

void	InitialiseForSolve (Vec initialSolution)

Protected Member Functions inherited from SimpleLinearEllipticSolver< DIM, DIM >
virtual c_matrix< double, 1 (ELEMENT_DIM+1), 1 (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, 1 > &rU, c_matrix< double, 1, SPACE_DIM > &rGradU, Element< ELEMENT_DIM, SPACE_DIM > *pElement)

virtual c_vector< double, 1 *(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, 1 > &rU, c_matrix< double, 1, SPACE_DIM > &rGradU, Element< ELEMENT_DIM, SPACE_DIM > *pElement)

void	SetupLinearSystem (Vec currentSolution, bool computeMatrix)

Protected Member Functions inherited from AbstractFeVolumeIntegralAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, true, true, INTERPOLATION_LEVEL >
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	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)

Private Attributes
double	mConstantInUSourceTerm

double	mLinearInUCoeffInSourceTerm

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

Protected Attributes inherited from SimpleLinearEllipticSolver< DIM, DIM >
AbstractLinearEllipticPde < ELEMENT_DIM, SPACE_DIM > *	mpEllipticPde

Protected Attributes inherited from AbstractAssemblerSolverHybrid< ELEMENT_DIM, SPACE_DIM, 1, NORMAL >
NaturalNeumannSurfaceTermAssembler < ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >	mNaturalNeumannSurfaceTermAssembler

BoundaryConditionsContainer < ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM > *	mpBoundaryConditions

Protected Attributes inherited from AbstractFeVolumeIntegralAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, true, true, INTERPOLATION_LEVEL >
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

Protected Attributes inherited from AbstractLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >
LinearSystem *	mpLinearSystem

AbstractTetrahedralMesh < ELEMENT_DIM, SPACE_DIM > *	mpMesh

Detailed Description

template<unsigned DIM>
class CellBasedPdeSolver< DIM >

A purpose-made elliptic solver that interpolates the source terms from node onto Gauss points, as for a cell-based simulation with PDEs the source will only be known at the cells (nodes), not the Gauss points.

Definition at line 48 of file CellBasedPdeSolver.hpp.

Constructor & Destructor Documentation

template<unsigned DIM>

CellBasedPdeSolver< DIM >::CellBasedPdeSolver	(	TetrahedralMesh< DIM, DIM > *	pMesh,
		AbstractLinearEllipticPde< DIM, DIM > *	pPde,
		BoundaryConditionsContainer< DIM, DIM, 1 > *	pBoundaryConditions
	)

Constructor.

Parameters

pMesh	pointer to the mesh
pPde	pointer to the PDE
pBoundaryConditions	pointer to the boundary conditions

Definition at line 41 of file CellBasedPdeSolver.cpp.

template<unsigned DIM>

CellBasedPdeSolver< DIM >::~CellBasedPdeSolver ( )

virtual

Destructor.

Definition at line 49 of file CellBasedPdeSolver.cpp.

Member Function Documentation

template<unsigned DIM>

c_matrix< double, 1 (DIM+1), 1 (DIM+1)> CellBasedPdeSolver< DIM >::ComputeMatrixTerm	(	c_vector< double, DIM+1 > &	rPhi,
		c_matrix< double, DIM, DIM+1 > &	rGradPhi,
		ChastePoint< DIM > &	rX,
		c_vector< double, 1 > &	rU,
		c_matrix< double, 1, DIM > &	rGradU,
		Element< DIM, DIM > *	pElement
	)

protectedvirtual

The SimpleLinearEllipticSolver version of this method is overloaded using the interpolated source term.

Parameters

rPhi	The basis functions, rPhi(i) = phi_i, i=1..numBases
rGradPhi	Basis gradients, rGradPhi(i,j) = d(phi_j)/d(X_i)
rX	The point in space
rU	The unknown as a vector, u(i) = u_i
rGradU	The gradient of the unknown as a matrix, rGradU(i,j) = d(u_i)/d(X_j)
pElement	Pointer to the element

Returns: The matrix term for the stiffness matrix

Definition at line 66 of file CellBasedPdeSolver.cpp.

template<unsigned DIM>

c_vector< double, 1 *(DIM+1)> CellBasedPdeSolver< DIM >::ComputeVectorTerm	(	c_vector< double, DIM+1 > &	rPhi,
		c_matrix< double, DIM, DIM+1 > &	rGradPhi,
		ChastePoint< DIM > &	rX,
		c_vector< double, 1 > &	rU,
		c_matrix< double, 1, DIM > &	rGradU,
		Element< DIM, DIM > *	pElement
	)

protectedvirtual

The SimpleLinearEllipticSolver version of this method is overloaded using the interpolated source term.

Parameters

rPhi
rGradPhi
rX
rU
rGradU
pElement

Returns: vector term.

Definition at line 54 of file CellBasedPdeSolver.cpp.

template<unsigned DIM>

void CellBasedPdeSolver< DIM >::IncrementInterpolatedQuantities	(	double	phiI,
		const Node< DIM > *	pNode
	)

protected

Overridden IncrementInterpolatedQuantities() method.

Parameters

phiI
pNode

Definition at line 96 of file CellBasedPdeSolver.cpp.

template<unsigned DIM>

void CellBasedPdeSolver< DIM >::InitialiseForSolve ( Vec initialSolution )

protectedvirtual

Create the linear system object if it hasn't been already. Can use an initial solution as PETSc template, or base it on the mesh size.

Parameters

initialSolution an initial guess

Reimplemented from AbstractLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >.

Definition at line 103 of file CellBasedPdeSolver.cpp.

References SimpleLinearEllipticSolver< ELEMENT_DIM, SPACE_DIM >::InitialiseForSolve().

template<unsigned DIM>

void CellBasedPdeSolver< DIM >::ResetInterpolatedQuantities ( void )

protectedvirtual

Overridden ResetInterpolatedQuantities() method.

Reimplemented from AbstractFeAssemblerCommon< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX, INTERPOLATION_LEVEL >.

Definition at line 89 of file CellBasedPdeSolver.cpp.

Member Data Documentation

template<unsigned DIM>

double CellBasedPdeSolver< DIM >::mConstantInUSourceTerm

private

The constant in u part of the source term, interpolated onto the current point.

Definition at line 54 of file CellBasedPdeSolver.hpp.

template<unsigned DIM>

double CellBasedPdeSolver< DIM >::mLinearInUCoeffInSourceTerm

private

The linear in u part of the source term, interpolated onto the current point.

Definition at line 57 of file CellBasedPdeSolver.hpp.

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

cell_based/src/population/pdes/CellBasedPdeSolver.hpp
cell_based/src/population/pdes/CellBasedPdeSolver.cpp

Public Member Functions

Protected Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

template<unsigned DIM> class CellBasedPdeSolver< DIM >

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation

template<unsigned DIM>
class CellBasedPdeSolver< DIM >