AveragedSourceParabolicPde< DIM > Class Template Reference

#include <AveragedSourceParabolicPde.hpp>

Inheritance diagram for AveragedSourceParabolicPde< DIM >:

Collaboration diagram for AveragedSourceParabolicPde< DIM >:

Public Member Functions
	AveragedSourceParabolicPde (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
virtual void	SetupSourceTerms (TetrahedralMesh< DIM, DIM > &rCoarseMesh, std::map< CellPtr, unsigned > *pCellPdeElementMap=nullptr)
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
double	GetUptakeRateForElement (unsigned elementIndex)
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
std::vector< double >	mCellDensityOnCoarseElements

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 AveragedSourceParabolicPde< 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 + 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.

The function rho(x) denotes the local density of non-apoptotic cells. This quantity is computed for each element of a 'coarse' finite element mesh that is passed to the method SetupSourceTerms() and stored in the member mCellDensityOnCoarseElements. For a point x, rho(x) is defined to be the number of non-apoptotic cells whose centres lie in each finite element containing that point, scaled by the area of that element.

Definition at line 66 of file AveragedSourceParabolicPde.hpp.

Constructor & Destructor Documentation

AveragedSourceParabolicPde()

template<unsigned DIM>

AveragedSourceParabolicPde< DIM >::AveragedSourceParabolicPde	(	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 40 of file AveragedSourceParabolicPde.cpp.

Member Function Documentation

ComputeDiffusionTerm()

template<unsigned DIM>

c_matrix< double, DIM, DIM > AveragedSourceParabolicPde< 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 178 of file AveragedSourceParabolicPde.cpp.

ComputeDuDtCoefficientFunction()

template<unsigned DIM>

double AveragedSourceParabolicPde< 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 153 of file AveragedSourceParabolicPde.cpp.

ComputeSourceTerm()

template<unsigned DIM>

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

override

Overridden ComputeSourceTerm() method.

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 159 of file AveragedSourceParabolicPde.cpp.

References AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetIndex().

ComputeSourceTermAtNode()

template<unsigned DIM>

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

override

Overridden ComputeSourceTermAtNode() method. That is never called.

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 171 of file AveragedSourceParabolicPde.cpp.

References NEVER_REACHED.

GetConstantCoefficient()

template<unsigned DIM>

double AveragedSourceParabolicPde< DIM >::GetConstantCoefficient

(

)

const

Returns

mConstantSourceCoefficient

Definition at line 62 of file AveragedSourceParabolicPde.cpp.

GetDiffusionCoefficient()

template<unsigned DIM>

double AveragedSourceParabolicPde< DIM >::GetDiffusionCoefficient

(

)

const

Returns

mDiffusionCoefficient

Definition at line 74 of file AveragedSourceParabolicPde.cpp.

GetDuDtCoefficient()

template<unsigned DIM>

double AveragedSourceParabolicPde< DIM >::GetDuDtCoefficient

(

)

const

Returns

mDuDtCoefficient

Definition at line 80 of file AveragedSourceParabolicPde.cpp.

GetLinearCoefficient()

template<unsigned DIM>

double AveragedSourceParabolicPde< DIM >::GetLinearCoefficient

(

)

const

Returns

mLinearSourceCoefficient

Definition at line 68 of file AveragedSourceParabolicPde.cpp.

GetScaleByCellVolume()

template<unsigned DIM>

bool AveragedSourceParabolicPde< DIM >::GetScaleByCellVolume

(

)

const

Returns

mScaleByCellVolume

Definition at line 86 of file AveragedSourceParabolicPde.cpp.

GetUptakeRateForElement()

template<unsigned DIM>

double AveragedSourceParabolicPde< DIM >::GetUptakeRateForElement

(

unsigned

elementIndex

)

Returns

the uptake rate.

Parameters

elementIndex

the element we wish to return the uptake rate for

Definition at line 184 of file AveragedSourceParabolicPde.cpp.

rGetCellPopulation()

template<unsigned DIM>

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

(

)

const

Returns

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

Definition at line 56 of file AveragedSourceParabolicPde.cpp.

serialize()

template<unsigned DIM>

template<class Archive >

void AveragedSourceParabolicPde< 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 81 of file AveragedSourceParabolicPde.hpp.

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

SetupSourceTerms()

template<unsigned DIM>

void AveragedSourceParabolicPde< DIM >::SetupSourceTerms ( TetrahedralMesh< DIM, DIM > &  rCoarseMesh, std::map< CellPtr, unsigned > *  pCellPdeElementMap = nullptr  )

virtual

Set up the source terms.

Todo:

this is identical to the one in AveragedSourceEllipticPde so refactor.

Parameters

rCoarseMesh	reference to the coarse mesh
pCellPdeElementMap	optional pointer to the map from cells to coarse elements

Definition at line 92 of file AveragedSourceParabolicPde.cpp.

References EXCEPTION, AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetContainingElementIndex(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetElement(), and AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetNumElements().

Friends And Related Symbol Documentation

boost::serialization::access

template<unsigned DIM>

friend class boost::serialization::access

friend

Needed for serialization.

Definition at line 73 of file AveragedSourceParabolicPde.hpp.

TestCellBasedParabolicPdes

template<unsigned DIM>

friend class TestCellBasedParabolicPdes

friend

Definition at line 68 of file AveragedSourceParabolicPde.hpp.

Member Data Documentation

mCellDensityOnCoarseElements

template<unsigned DIM>

std::vector<double> AveragedSourceParabolicPde< DIM >::mCellDensityOnCoarseElements

protected

Vector of averaged cell densities on elements of the coarse mesh.

Definition at line 113 of file AveragedSourceParabolicPde.hpp.

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

mConstantSourceCoefficient

template<unsigned DIM>

double AveragedSourceParabolicPde< DIM >::mConstantSourceCoefficient

protected

Coefficient of constant source term.

Definition at line 98 of file AveragedSourceParabolicPde.hpp.

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

mDiffusionCoefficient

template<unsigned DIM>

double AveragedSourceParabolicPde< DIM >::mDiffusionCoefficient

protected

Diffusion coefficient.

Definition at line 104 of file AveragedSourceParabolicPde.hpp.

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

mDuDtCoefficient

template<unsigned DIM>

double AveragedSourceParabolicPde< DIM >::mDuDtCoefficient

protected

Coefficient of rate of change term.

Definition at line 107 of file AveragedSourceParabolicPde.hpp.

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

mLinearSourceCoefficient

template<unsigned DIM>

double AveragedSourceParabolicPde< DIM >::mLinearSourceCoefficient

protected

Coefficient of linear source term.

Definition at line 101 of file AveragedSourceParabolicPde.hpp.

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

mrCellPopulation

template<unsigned DIM>

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

protected

The cell population member.

Definition at line 95 of file AveragedSourceParabolicPde.hpp.

mScaleByCellVolume

template<unsigned DIM>

bool AveragedSourceParabolicPde< DIM >::mScaleByCellVolume

protected

Whether to scale terms by cell volume

Definition at line 110 of file AveragedSourceParabolicPde.hpp.

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

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

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