PdeAndBoundaryConditions< DIM > Class Template Reference

#include <PdeAndBoundaryConditions.hpp>

Collaboration diagram for PdeAndBoundaryConditions< DIM >:

[legend]

List of all members.

Public Member Functions
	PdeAndBoundaryConditions (AbstractLinearEllipticPde< DIM, DIM > *pPde=NULL, AbstractBoundaryCondition< DIM > *pBoundaryCondition=NULL, bool isNeumannBoundaryCondition=true, Vec solution=NULL, bool deleteMemberPointersInDestructor=false)
	~PdeAndBoundaryConditions ()
AbstractLinearEllipticPde< DIM, DIM > *	GetPde ()
AbstractBoundaryCondition< DIM > *	GetBoundaryCondition () const
Vec	GetSolution ()
Vec	GetSolution () const
void	SetSolution (Vec solution)
bool	IsNeumannBoundaryCondition ()
bool	HasAveragedSourcePde ()
void	DestroySolution ()
void	SetUpSourceTermsForAveragedSourcePde (TetrahedralMesh< DIM, DIM > *pMesh, std::map< CellPtr, unsigned > *pCellPdeElementMap=NULL)
void	SetDependentVariableName (const std::string &rName)
std::string &	rGetDependentVariableName ()
Private Member Functions
template<class Archive >
void	serialize (Archive &archive, const unsigned int version)
Private Attributes
AbstractLinearEllipticPde< DIM, DIM > *	mpPde
AbstractBoundaryCondition< DIM > *	mpBoundaryCondition
bool	mIsNeumannBoundaryCondition
Vec	mSolution
bool	mDeleteMemberPointersInDestructor
std::string	mDependentVariableName
Friends
class	TestPdeAndBoundaryConditions
class	boost::serialization::access

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Detailed Description

template<unsigned DIM>
class PdeAndBoundaryConditions< DIM >

A helper class for use in cell-based simulations with PDEs. The class contains a pointer to a linear elliptic PDE, which is to be solved on the domain defined by the cell population. The class also contains information describing the boundary condition that is to be imposed when solving the PDE. Currently we allow Neumann (imposed flux) or Dirichlet (imposed value) boundary conditions. The boundary condition may be constant on the boundary or vary spatially and/or temporally. In cell-based simulations with PDEs, one or more of these objects are accessed via the CellBasedPdeHandler class.

Definition at line 59 of file PdeAndBoundaryConditions.hpp.

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Constructor & Destructor Documentation

template<unsigned DIM>

PdeAndBoundaryConditions< DIM >::PdeAndBoundaryConditions	(	AbstractLinearEllipticPde< DIM, DIM > *	pPde = NULL,
		AbstractBoundaryCondition< DIM > *	pBoundaryCondition = NULL,
		bool	isNeumannBoundaryCondition = true,
		Vec	solution = NULL,
		bool	deleteMemberPointersInDestructor = false
	)			[inline]

Constructor.

Parameters:

	pPde	A pointer to a linear elliptic PDE object (defaults to NULL)
	pBoundaryCondition	A pointer to an abstract boundary condition (defaults to NULL, corresponding to a constant boundary condition with value zero)
	isNeumannBoundaryCondition	Whether the boundary condition is Neumann (defaults to true)
	solution	A solution vector (defaults to NULL)
	deleteMemberPointersInDestructor	whether to delete member pointers in the destructor (defaults to false)

Definition at line 39 of file PdeAndBoundaryConditions.cpp.

References PdeAndBoundaryConditions< DIM >::mSolution.

template<unsigned DIM>

PdeAndBoundaryConditions< DIM >::~PdeAndBoundaryConditions

(

)

[inline]

Destructor.

Definition at line 58 of file PdeAndBoundaryConditions.cpp.

References PdeAndBoundaryConditions< DIM >::DestroySolution(), PdeAndBoundaryConditions< DIM >::mDeleteMemberPointersInDestructor, PdeAndBoundaryConditions< DIM >::mpBoundaryCondition, and PdeAndBoundaryConditions< DIM >::mpPde.

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Member Function Documentation

template<unsigned DIM>

void PdeAndBoundaryConditions< DIM >::DestroySolution

(

)

[inline]

Call PetscTools::Destroy on mSolution.

Definition at line 113 of file PdeAndBoundaryConditions.cpp.

References PetscTools::Destroy(), and PdeAndBoundaryConditions< DIM >::mSolution.

Referenced by CellBasedPdeHandler< DIM >::SolvePdeAndWriteResultsToFile(), and PdeAndBoundaryConditions< DIM >::~PdeAndBoundaryConditions().

template<unsigned DIM>

AbstractBoundaryCondition< DIM > * PdeAndBoundaryConditions< DIM >::GetBoundaryCondition

(

)

const [inline]

Returns:

mpBoundaryCondition

Definition at line 77 of file PdeAndBoundaryConditions.cpp.

References PdeAndBoundaryConditions< DIM >::mpBoundaryCondition.

Referenced by CellBasedPdeHandler< DIM >::ConstructBoundaryConditionsContainer().

template<unsigned DIM>

AbstractLinearEllipticPde< DIM, DIM > * PdeAndBoundaryConditions< DIM >::GetPde

(

)

[inline]

Returns:

mpPde

Definition at line 71 of file PdeAndBoundaryConditions.cpp.

References PdeAndBoundaryConditions< DIM >::mpPde.

Referenced by CellBasedPdeHandler< DIM >::SolvePdeAndWriteResultsToFile().

template<unsigned DIM>

Vec PdeAndBoundaryConditions< DIM >::GetSolution

(

)

const [inline]

Returns:

mSolution (used in archiving)

Definition at line 89 of file PdeAndBoundaryConditions.cpp.

References PdeAndBoundaryConditions< DIM >::mSolution.

template<unsigned DIM>

Vec PdeAndBoundaryConditions< DIM >::GetSolution

(

)

[inline]

Returns:

mSolution

Definition at line 83 of file PdeAndBoundaryConditions.cpp.

References PdeAndBoundaryConditions< DIM >::mSolution.

Referenced by CellBasedPdeHandler< DIM >::GetPdeSolutionAtPoint(), CellBasedPdeHandler< DIM >::SolvePdeAndWriteResultsToFile(), and CellBasedPdeHandler< DIM >::WritePdeSolution().

template<unsigned DIM>

bool PdeAndBoundaryConditions< DIM >::HasAveragedSourcePde

(

)

[inline]

Returns:

whether the PDE is of type AveragedSourcePde

Definition at line 107 of file PdeAndBoundaryConditions.cpp.

References PdeAndBoundaryConditions< DIM >::mpPde.

Referenced by PdeAndBoundaryConditions< DIM >::SetUpSourceTermsForAveragedSourcePde(), and CellBasedPdeHandler< DIM >::SolvePdeAndWriteResultsToFile().

template<unsigned DIM>

bool PdeAndBoundaryConditions< DIM >::IsNeumannBoundaryCondition

(

)

[inline]

Returns:

mIsNeumannBoundaryCondition

Definition at line 101 of file PdeAndBoundaryConditions.cpp.

References PdeAndBoundaryConditions< DIM >::mIsNeumannBoundaryCondition.

Referenced by CellBasedPdeHandler< DIM >::ConstructBoundaryConditionsContainer().

template<unsigned DIM>

std::string & PdeAndBoundaryConditions< DIM >::rGetDependentVariableName

(

)

[inline]

Get the name of the dependent variable.

Returns:

the name

Definition at line 135 of file PdeAndBoundaryConditions.cpp.

References PdeAndBoundaryConditions< DIM >::mDependentVariableName.

Referenced by CellBasedPdeHandler< DIM >::AddPdeAndBc(), and CellBasedPdeHandler< DIM >::WritePdeSolution().

template<unsigned DIM>

template<class Archive >

void PdeAndBoundaryConditions< DIM >::serialize	(	Archive &	archive,
		const unsigned int	version
	)			[inline, private]

Serialize the PDE object.

Parameters:

	archive	the archive
	version	the current version of this class

Definition at line 74 of file PdeAndBoundaryConditions.hpp.

References PdeAndBoundaryConditions< DIM >::mDependentVariableName, PdeAndBoundaryConditions< DIM >::mIsNeumannBoundaryCondition, PdeAndBoundaryConditions< DIM >::mpBoundaryCondition, and PdeAndBoundaryConditions< DIM >::mpPde.

template<unsigned DIM>

void PdeAndBoundaryConditions< DIM >::SetDependentVariableName

(

const std::string &

rName

)

[inline]

Set the name of the dependent variable.

Parameters:

rName

the name.

Definition at line 129 of file PdeAndBoundaryConditions.cpp.

References PdeAndBoundaryConditions< DIM >::mDependentVariableName.

template<unsigned DIM>

void PdeAndBoundaryConditions< DIM >::SetSolution

(

Vec

solution

)

[inline]

Set mSolution.

Parameters:

solution

the current solution

Definition at line 95 of file PdeAndBoundaryConditions.cpp.

References PdeAndBoundaryConditions< DIM >::mSolution.

Referenced by CellBasedPdeHandler< DIM >::SolvePdeAndWriteResultsToFile().

template<unsigned DIM>

void PdeAndBoundaryConditions< DIM >::SetUpSourceTermsForAveragedSourcePde	(	TetrahedralMesh< DIM, DIM > *	pMesh,
		std::map< CellPtr, unsigned > *	pCellPdeElementMap = NULL
	)			[inline]

In the case where mpPde is of type AveragedSourcePde, set the source terms using the information in the given mesh.

Parameters:

	pMesh	Pointer to a tetrahedral mesh
	pCellPdeElementMap	map between cells and elements, from CellBasedPdeHandler

Definition at line 122 of file PdeAndBoundaryConditions.cpp.

References PdeAndBoundaryConditions< DIM >::HasAveragedSourcePde(), and PdeAndBoundaryConditions< DIM >::mpPde.

Referenced by CellBasedPdeHandler< DIM >::SolvePdeAndWriteResultsToFile().

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Friends And Related Function Documentation

template<unsigned DIM>

friend class boost::serialization::access [friend]

Needed for serialization.

Definition at line 66 of file PdeAndBoundaryConditions.hpp.

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Member Data Documentation

template<unsigned DIM>

bool PdeAndBoundaryConditions< DIM >::mDeleteMemberPointersInDestructor [private]

Whether to delete member pointers in the destructor (used in archiving).

Definition at line 96 of file PdeAndBoundaryConditions.hpp.

Referenced by PdeAndBoundaryConditions< DIM >::~PdeAndBoundaryConditions().

template<unsigned DIM>

std::string PdeAndBoundaryConditions< DIM >::mDependentVariableName [private]

For use in PDEs where we know what the quantity for which we are solving is called, e.g. oxygen concentration.

Definition at line 101 of file PdeAndBoundaryConditions.hpp.

Referenced by PdeAndBoundaryConditions< DIM >::rGetDependentVariableName(), PdeAndBoundaryConditions< DIM >::serialize(), and PdeAndBoundaryConditions< DIM >::SetDependentVariableName().

template<unsigned DIM>

bool PdeAndBoundaryConditions< DIM >::mIsNeumannBoundaryCondition [private]

Whether the boundary condition is Neumann (false corresponds to a Dirichlet boundary condition).

Definition at line 90 of file PdeAndBoundaryConditions.hpp.

Referenced by PdeAndBoundaryConditions< DIM >::IsNeumannBoundaryCondition(), and PdeAndBoundaryConditions< DIM >::serialize().

template<unsigned DIM>

AbstractBoundaryCondition<DIM>* PdeAndBoundaryConditions< DIM >::mpBoundaryCondition [private]

Pointer to a boundary condition object.

Definition at line 87 of file PdeAndBoundaryConditions.hpp.

Referenced by PdeAndBoundaryConditions< DIM >::GetBoundaryCondition(), PdeAndBoundaryConditions< DIM >::serialize(), and PdeAndBoundaryConditions< DIM >::~PdeAndBoundaryConditions().

template<unsigned DIM>

AbstractLinearEllipticPde<DIM,DIM>* PdeAndBoundaryConditions< DIM >::mpPde [private]

Pointer to a linear elliptic PDE object.

Definition at line 84 of file PdeAndBoundaryConditions.hpp.

Referenced by PdeAndBoundaryConditions< DIM >::GetPde(), PdeAndBoundaryConditions< DIM >::HasAveragedSourcePde(), PdeAndBoundaryConditions< DIM >::serialize(), PdeAndBoundaryConditions< DIM >::SetUpSourceTermsForAveragedSourcePde(), and PdeAndBoundaryConditions< DIM >::~PdeAndBoundaryConditions().

template<unsigned DIM>

Vec PdeAndBoundaryConditions< DIM >::mSolution [private]

The solution to the PDE problem, for use as an initial guess when solving at the next time step.

Definition at line 93 of file PdeAndBoundaryConditions.hpp.

Referenced by PdeAndBoundaryConditions< DIM >::DestroySolution(), PdeAndBoundaryConditions< DIM >::GetSolution(), PdeAndBoundaryConditions< DIM >::PdeAndBoundaryConditions(), and PdeAndBoundaryConditions< DIM >::SetSolution().

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

• cell_based/src/population/pdes/PdeAndBoundaryConditions.hpp
• cell_based/src/population/pdes/PdeAndBoundaryConditions.cpp