#include <CellwiseSourceParabolicPde.hpp>

Inheritance diagram for CellwiseSourceParabolicPde< DIM >:

Collaboration diagram for CellwiseSourceParabolicPde< DIM >:

Public Member Functions
	CellwiseSourceParabolicPde (AbstractCellPopulation< DIM, DIM > &rCellPopulation, double duDtCoefficient=1.0, double diffusionCoefficient=1.0, double sourceCoefficient=0.0)

const AbstractCellPopulation< DIM > &	rGetCellPopulation () const

virtual double	ComputeDuDtCoefficientFunction (const ChastePoint< DIM > &rX)

virtual double	ComputeSourceTerm (const ChastePoint< DIM > &rX, double u, Element< DIM, DIM > *pElement=NULL)

virtual double	ComputeSourceTermAtNode (const Node< DIM > &rNode, double u)

virtual c_matrix< double, DIM, DIM >	ComputeDiffusionTerm (const ChastePoint< DIM > &rX, Element< DIM, DIM > *pElement=NULL)

Public Member Functions inherited from AbstractLinearParabolicPde< DIM, DIM >
	AbstractLinearParabolicPde ()

virtual	~AbstractLinearParabolicPde ()

virtual double	ComputeDuDtCoefficientFunction (const ChastePoint< SPACE_DIM > &rX)=0

virtual double	ComputeSourceTerm (const ChastePoint< SPACE_DIM > &rX, double u, Element< ELEMENT_DIM, SPACE_DIM > *pElement=nullptr)=0

virtual double	ComputeSourceTermAtNode (const Node< SPACE_DIM > &rNode, double u)

virtual c_matrix< double, SPACE_DIM, SPACE_DIM >	ComputeDiffusionTerm (const ChastePoint< SPACE_DIM > &rX, Element< ELEMENT_DIM, SPACE_DIM > *pElement=NULL)=0

Public Member Functions inherited from AbstractLinearPde< ELEMENT_DIM, SPACE_DIM >
	AbstractLinearPde ()

virtual	~AbstractLinearPde ()

Protected Attributes
AbstractCellPopulation< DIM, DIM > &	mrCellPopulation

double	mDuDtCoefficient

double	mDiffusionCoefficient

double	mSourceCoefficient

Private Member Functions
template<class Archive >
void	serialize (Archive &archive, const unsigned int version)

Friends
class	TestCellBasedParabolicPdes

class	boost::serialization::access

Detailed Description

template<unsigned DIM>
class CellwiseSourceParabolicPde< DIM >

A parabolic PDE to be solved numerically using the finite element method, for coupling to a cell-based simulation.

The PDE takes the form

c*du/dt = Grad.(D*Grad(u)) + k*u*rho(x),

where the scalars c, D and k are specified by the members mDuDtCoefficient, mDiffusionCoefficient and mSourceCoefficient, respectively. Their values must be set in the constructor.

For a node of the finite element mesh with location x, the function rho(x) equals one if there is a non-apoptotic cell associated with x, and zero otherwise. Here, 'associated with' takes a different meaning for each cell population class, and is encoded in the method IsPdeNodeAssociatedWithNonApoptoticCell().

Definition at line 63 of file CellwiseSourceParabolicPde.hpp.

Constructor & Destructor Documentation

template<unsigned DIM>

CellwiseSourceParabolicPde< DIM >::CellwiseSourceParabolicPde	(	AbstractCellPopulation< DIM, DIM > &	rCellPopulation,
		double	duDtCoefficient = `1.0`,
		double	diffusionCoefficient = `1.0`,
		double	sourceCoefficient = `0.0`
	)

Constructor.

Parameters

rCellPopulation	reference to the cell population
duDtCoefficient	rate of reaction (defaults to 1.0)
diffusionCoefficient	rate of diffusion (defaults to 1.0)
sourceCoefficient	the source term coefficient (defaults to 0.0)

Definition at line 39 of file CellwiseSourceParabolicPde.cpp.

Member Function Documentation

template<unsigned DIM>

c_matrix< double, DIM, DIM > CellwiseSourceParabolicPde< DIM >::ComputeDiffusionTerm	(	const ChastePoint< DIM > &	rX,
		Element< DIM, DIM > *	pElement = `NULL`
	)

virtual

Overridden ComputeDiffusionTerm() method.

Parameters

rX	the point in space at which the diffusion term is computed
pElement	the mesh element that x is contained in (optional; defaults to NULL).

Returns: a matrix.

Definition at line 86 of file CellwiseSourceParabolicPde.cpp.

References EXPORT_TEMPLATE_CLASS_SAME_DIMS, and CellwiseSourceParabolicPde< DIM >::mDiffusionCoefficient.

template<unsigned DIM>

double CellwiseSourceParabolicPde< DIM >::ComputeDuDtCoefficientFunction ( const ChastePoint< DIM > & rX )

virtual

Overridden ComputeDuDtCoefficientFunction() method.

Returns: the function c(x) in "c(x) du/dt = Grad.(DiffusionTerm(x)*Grad(u))+LinearSourceTerm(x)+NonlinearSourceTerm(x, u)"

Parameters

rX	the point in space at which the function c is computed

Definition at line 57 of file CellwiseSourceParabolicPde.cpp.

References CellwiseSourceParabolicPde< DIM >::mDuDtCoefficient.

template<unsigned DIM>

double CellwiseSourceParabolicPde< DIM >::ComputeSourceTerm	(	const ChastePoint< DIM > &	rX,
		double	u,
		Element< DIM, DIM > *	pElement = `NULL`
	)

virtual

Overridden ComputeSourceTerm() method. That is never called.

Returns: computed source term.

Parameters

rX	the point in space at which the nonlinear source term is computed
u	the value of the dependent variable at the point
pElement	the mesh element that x is contained in (optional; defaults to NULL).

Definition at line 64 of file CellwiseSourceParabolicPde.cpp.

References NEVER_REACHED.

template<unsigned DIM>

double CellwiseSourceParabolicPde< DIM >::ComputeSourceTermAtNode	(	const Node< DIM > &	rNode,
		double	u
	)

virtual

Overridden ComputeSourceTermAtNode() method.

Note that for CellWise Parabolic PDEs used with CellBasedParabolicPdeSolver this method returns the coefficient of the linear component of the source term.