CellBasedSimulationWithPdesAssembler< DIM > Class Template Reference

#include <CellBasedSimulationWithPdesAssembler.hpp>

Inheritance diagram for CellBasedSimulationWithPdesAssembler< DIM >:

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Collaboration diagram for CellBasedSimulationWithPdesAssembler< DIM >:

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List of all members.

Public Member Functions
	CellBasedSimulationWithPdesAssembler (TetrahedralMesh< DIM, DIM > *pMesh, AbstractLinearEllipticPde< DIM, DIM > *pPde, BoundaryConditionsContainer< DIM, DIM, 1 > *pBoundaryConditions, unsigned numQuadPoints=2)
	~CellBasedSimulationWithPdesAssembler ()
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)
Private Attributes
double	mConstantInUSourceTerm
double	mLinearInUCoeffInSourceTerm

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Detailed Description

template<unsigned DIM>
class CellBasedSimulationWithPdesAssembler< DIM >

CellBasedSimulationWithPdesAssembler

This is a purpose made elliptic assembler 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 47 of file CellBasedSimulationWithPdesAssembler.hpp.

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Constructor & Destructor Documentation

template<unsigned DIM>

CellBasedSimulationWithPdesAssembler< DIM >::CellBasedSimulationWithPdesAssembler	(	TetrahedralMesh< DIM, DIM > *	pMesh,
		AbstractLinearEllipticPde< DIM, DIM > *	pPde,
		BoundaryConditionsContainer< DIM, DIM, 1 > *	pBoundaryConditions,
		unsigned	numQuadPoints = 2
	)			[inline]

Constructor

Parameters:

	pMesh	pointer to the mesh
	pPde	pointer to the PDE
	pBoundaryConditions	pointer to the boundary conditions
	numQuadPoints	number of quadrature points (defaults to 2)

Definition at line 36 of file CellBasedSimulationWithPdesAssembler.cpp.

template<unsigned DIM>

CellBasedSimulationWithPdesAssembler< DIM >::~CellBasedSimulationWithPdesAssembler

(

)

[inline]

Destructor.

Definition at line 45 of file CellBasedSimulationWithPdesAssembler.cpp.

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Member Function Documentation

template<unsigned DIM>

c_vector< double, 1 *(DIM+1)> CellBasedSimulationWithPdesAssembler< 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
	)			[inline, protected, virtual]

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

Parameters:

	rPhi
	rGradPhi
	rX
	rU
	rGradU
	pElement

Definition at line 50 of file CellBasedSimulationWithPdesAssembler.cpp.

References CellBasedSimulationWithPdesAssembler< DIM >::mConstantInUSourceTerm.

template<unsigned DIM>

c_matrix< double, 1 *(DIM+1), 1 *(DIM+1)> CellBasedSimulationWithPdesAssembler< 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
	)			[inline, protected, virtual]

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

Definition at line 62 of file CellBasedSimulationWithPdesAssembler.cpp.

References CellBasedSimulationWithPdesAssembler< DIM >::mLinearInUCoeffInSourceTerm, and SimpleLinearEllipticSolver< DIM, DIM >::mpEllipticPde.

template<unsigned DIM>

void CellBasedSimulationWithPdesAssembler< DIM >::ResetInterpolatedQuantities

(

void

)

[inline, protected, virtual]

Overridden ResetInterpolatedQuantities() method.

Reimplemented from AbstractFeObjectAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, true, true, INTERPOLATION_LEVEL >.

Definition at line 85 of file CellBasedSimulationWithPdesAssembler.cpp.

References CellBasedSimulationWithPdesAssembler< DIM >::mConstantInUSourceTerm, and CellBasedSimulationWithPdesAssembler< DIM >::mLinearInUCoeffInSourceTerm.

template<unsigned DIM>

void CellBasedSimulationWithPdesAssembler< DIM >::IncrementInterpolatedQuantities	(	double	phiI,
		const Node< DIM > *	pNode
	)			[inline, protected]

Overridden IncrementInterpolatedQuantities() method.

Parameters:

	phiI
	pNode

Definition at line 92 of file CellBasedSimulationWithPdesAssembler.cpp.

References CellBasedSimulationWithPdesAssembler< DIM >::mConstantInUSourceTerm, CellBasedSimulationWithPdesAssembler< DIM >::mLinearInUCoeffInSourceTerm, and SimpleLinearEllipticSolver< DIM, DIM >::mpEllipticPde.

template<unsigned DIM>

void CellBasedSimulationWithPdesAssembler< DIM >::InitialiseForSolve

(

Vec

initialSolution

)

[inline, protected, virtual]

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 SimpleLinearEllipticSolver< DIM, DIM >.

Definition at line 99 of file CellBasedSimulationWithPdesAssembler.cpp.

References SimpleLinearEllipticSolver< ELEMENT_DIM, SPACE_DIM >::InitialiseForSolve(), AbstractLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpLinearSystem, and LinearSystem::SetMatrixIsSymmetric().

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Member Data Documentation

template<unsigned DIM>

double CellBasedSimulationWithPdesAssembler< DIM >::mConstantInUSourceTerm [private]

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

Definition at line 56 of file CellBasedSimulationWithPdesAssembler.hpp.

Referenced by CellBasedSimulationWithPdesAssembler< DIM >::ComputeVectorTerm(), CellBasedSimulationWithPdesAssembler< DIM >::IncrementInterpolatedQuantities(), and CellBasedSimulationWithPdesAssembler< DIM >::ResetInterpolatedQuantities().

template<unsigned DIM>

double CellBasedSimulationWithPdesAssembler< DIM >::mLinearInUCoeffInSourceTerm [private]

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

Definition at line 62 of file CellBasedSimulationWithPdesAssembler.hpp.

Referenced by CellBasedSimulationWithPdesAssembler< DIM >::ComputeMatrixTerm(), CellBasedSimulationWithPdesAssembler< DIM >::IncrementInterpolatedQuantities(), and CellBasedSimulationWithPdesAssembler< DIM >::ResetInterpolatedQuantities().

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

• cell_based/src/simulation/CellBasedSimulationWithPdesAssembler.hpp
• cell_based/src/simulation/CellBasedSimulationWithPdesAssembler.cpp