CellwiseSourceParabolicPde< DIM > Class Template Reference

#include <CellwiseSourceParabolicPde.hpp>

Inheritance diagram for CellwiseSourceParabolicPde< DIM >:

Collaboration diagram for CellwiseSourceParabolicPde< DIM >:

Public Member Functions
	CellwiseSourceParabolicPde (AbstractCellPopulation< DIM, DIM > &rCellPopulation, double constantSourceCoefficient=0.0, double linearSourceCoefficient=0.0, double diffusionCoefficient=1.0, double duDtCoefficient=1.0, bool scaleByCellVolume=false)
const AbstractCellPopulation< DIM > &	rGetCellPopulation () const
double	GetConstantCoefficient () const
double	GetLinearCoefficient () const
double	GetDiffusionCoefficient () const
double	GetDuDtCoefficient () const
bool	GetScaleByCellVolume () const
double	ComputeDuDtCoefficientFunction (const ChastePoint< DIM > &rX) override
double	ComputeSourceTerm (const ChastePoint< DIM > &rX, double u, Element< DIM, DIM > *pElement) override
double	ComputeSourceTermAtNode (const Node< DIM > &rNode, double u) override
c_matrix< double, DIM, DIM >	ComputeDiffusionTerm (const ChastePoint< DIM > &rX, Element< DIM, DIM > *pElement=nullptr) override
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)=0
Public Member Functions inherited from AbstractLinearPde< ELEMENT_DIM, SPACE_DIM >
	AbstractLinearPde ()
virtual	~AbstractLinearPde ()

Protected Attributes
AbstractCellPopulation< DIM, DIM > &	mrCellPopulation
double	mConstantSourceCoefficient
double	mLinearSourceCoefficient
double	mDiffusionCoefficient
double	mDuDtCoefficient
bool	mScaleByCellVolume

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)) + a*u*rho(x) + b*rho(x),

where the scalars c, D, a and b are specified by the members mDuDtCoefficient, mDiffusionCoefficient, mLinearSourceCoefficient and mConstantSourceCoefficient, 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

CellwiseSourceParabolicPde()

template<unsigned DIM>

CellwiseSourceParabolicPde< DIM >::CellwiseSourceParabolicPde	(	AbstractCellPopulation< DIM, DIM > &	rCellPopulation,
		double	constantSourceCoefficient = 0.0,
		double	linearSourceCoefficient = 0.0,
		double	diffusionCoefficient = 1.0,
		double	duDtCoefficient = 1.0,
		bool	scaleByCellVolume = false
	)

Constructor.

Parameters

rCellPopulation	reference to the cell population
constantSourceCoefficient	the constant source term coefficient (defaults to 0.0)
linearSourceCoefficient	the linear source term coefficient (defaults to 0.0)
diffusionCoefficient	the rate of diffusion (defaults to 1.0)
duDtCoefficient	rate of reaction (defaults to 1.0)
scaleByCellVolume	whether to scale by cell volume (defaults to false)

Definition at line 39 of file CellwiseSourceParabolicPde.cpp.

Member Function Documentation

ComputeDiffusionTerm()

template<unsigned DIM>

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

override

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 140 of file CellwiseSourceParabolicPde.cpp.

ComputeDuDtCoefficientFunction()

template<unsigned DIM>

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

override

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 91 of file CellwiseSourceParabolicPde.cpp.

ComputeSourceTerm()

template<unsigned DIM>

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

override

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 98 of file CellwiseSourceParabolicPde.cpp.

References NEVER_REACHED.

ComputeSourceTermAtNode()

template<unsigned DIM>

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

override

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.

Returns

computed source term at a node.

Parameters

rNode	the node at which the nonlinear source term is computed
u	the value of the dependent variable at the node

Definition at line 105 of file CellwiseSourceParabolicPde.cpp.

References EXCEPTION, and Node< SPACE_DIM >::GetIndex().

GetConstantCoefficient()

template<unsigned DIM>

double CellwiseSourceParabolicPde< DIM >::GetConstantCoefficient

(

)

const

Returns

mConstantSourceCoefficient

Definition at line 61 of file CellwiseSourceParabolicPde.cpp.

GetDiffusionCoefficient()

template<unsigned DIM>

double CellwiseSourceParabolicPde< DIM >::GetDiffusionCoefficient

(

)

const

Returns

mDiffusionCoefficient

Definition at line 73 of file CellwiseSourceParabolicPde.cpp.

GetDuDtCoefficient()

template<unsigned DIM>

double CellwiseSourceParabolicPde< DIM >::GetDuDtCoefficient

(

)

const

Returns

mDuDtCoefficient

Definition at line 79 of file CellwiseSourceParabolicPde.cpp.

GetLinearCoefficient()

template<unsigned DIM>

double CellwiseSourceParabolicPde< DIM >::GetLinearCoefficient

(

)

const

Returns

mLinearSourceCoefficient

Definition at line 67 of file CellwiseSourceParabolicPde.cpp.

GetScaleByCellVolume()

template<unsigned DIM>

bool CellwiseSourceParabolicPde< DIM >::GetScaleByCellVolume

(

)

const

Returns

mScaleByCellVolume

Definition at line 85 of file CellwiseSourceParabolicPde.cpp.

rGetCellPopulation()

template<unsigned DIM>

const AbstractCellPopulation< DIM, DIM > & CellwiseSourceParabolicPde< DIM >::rGetCellPopulation

(

)

const

Returns

const reference to the cell population (used in archiving).

Definition at line 55 of file CellwiseSourceParabolicPde.cpp.

serialize()

template<unsigned DIM>

template<class Archive >

void CellwiseSourceParabolicPde< DIM >::serialize ( Archive &  archive, const unsigned int  version  )

inlineprivate

Serialize the PDE and its member variables.

Parameters

archive	the archive
version	the current version of this class

Definition at line 78 of file CellwiseSourceParabolicPde.hpp.

References CellwiseSourceParabolicPde< DIM >::mConstantSourceCoefficient, CellwiseSourceParabolicPde< DIM >::mDiffusionCoefficient, CellwiseSourceParabolicPde< DIM >::mDuDtCoefficient, CellwiseSourceParabolicPde< DIM >::mLinearSourceCoefficient, and CellwiseSourceParabolicPde< DIM >::mScaleByCellVolume.

Friends And Related Symbol Documentation

boost::serialization::access

template<unsigned DIM>

friend class boost::serialization::access

friend

Needed for serialization.

Definition at line 70 of file CellwiseSourceParabolicPde.hpp.

TestCellBasedParabolicPdes

template<unsigned DIM>

friend class TestCellBasedParabolicPdes

friend

Definition at line 65 of file CellwiseSourceParabolicPde.hpp.

Member Data Documentation

mConstantSourceCoefficient

template<unsigned DIM>

double CellwiseSourceParabolicPde< DIM >::mConstantSourceCoefficient

protected

Coefficient of constant source term.

Definition at line 94 of file CellwiseSourceParabolicPde.hpp.

Referenced by CellwiseSourceParabolicPde< DIM >::serialize().

mDiffusionCoefficient

template<unsigned DIM>

double CellwiseSourceParabolicPde< DIM >::mDiffusionCoefficient

protected

Diffusion coefficient.

Definition at line 100 of file CellwiseSourceParabolicPde.hpp.

Referenced by CellwiseSourceParabolicPde< DIM >::serialize().

mDuDtCoefficient

template<unsigned DIM>

double CellwiseSourceParabolicPde< DIM >::mDuDtCoefficient

protected

Coefficient of rate of change term.

Definition at line 103 of file CellwiseSourceParabolicPde.hpp.

Referenced by CellwiseSourceParabolicPde< DIM >::serialize().

mLinearSourceCoefficient

template<unsigned DIM>

double CellwiseSourceParabolicPde< DIM >::mLinearSourceCoefficient

protected

Coefficient of linear source term.

Definition at line 97 of file CellwiseSourceParabolicPde.hpp.

Referenced by CellwiseSourceParabolicPde< DIM >::serialize().

mrCellPopulation

template<unsigned DIM>

AbstractCellPopulation<DIM, DIM>& CellwiseSourceParabolicPde< DIM >::mrCellPopulation

protected

The cell population member.

Definition at line 91 of file CellwiseSourceParabolicPde.hpp.

mScaleByCellVolume

template<unsigned DIM>

bool CellwiseSourceParabolicPde< DIM >::mScaleByCellVolume

protected

Whether to scale terms by cell volume.

Definition at line 106 of file CellwiseSourceParabolicPde.hpp.

Referenced by CellwiseSourceParabolicPde< DIM >::serialize().

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

• cell_based/src/cell_based_pde/pdes/CellwiseSourceParabolicPde.hpp
• cell_based/src/cell_based_pde/pdes/CellwiseSourceParabolicPde.cpp