#include <AbstractPdeModifier.hpp>

Inheritance diagram for AbstractPdeModifier< DIM >:

Collaboration diagram for AbstractPdeModifier< DIM >:

Public Member Functions
	AbstractPdeModifier (boost::shared_ptr< AbstractLinearPde< DIM, DIM > > pPde=NULL, boost::shared_ptr< AbstractBoundaryCondition< DIM > > pBoundaryCondition=boost::shared_ptr< AbstractBoundaryCondition< DIM > >(), bool isNeumannBoundaryCondition=true, Vec solution=nullptr)

	~AbstractPdeModifier () override

boost::shared_ptr< AbstractLinearPde< DIM, DIM > >	GetPde ()

boost::shared_ptr< AbstractBoundaryCondition< DIM > >	GetBoundaryCondition ()

bool	IsNeumannBoundaryCondition () const

void	SetDependentVariableName (const std::string &rName)

std::string &	rGetDependentVariableName ()

bool	HasAveragedSourcePde ()

void	SetUpSourceTermsForAveragedSourcePde (TetrahedralMesh< DIM, DIM > pMesh, std::map< CellPtr, unsigned > pCellPdeElementMap=nullptr)

Vec	GetSolution ()

Vec	GetSolution () const

TetrahedralMesh< DIM, DIM > *	GetFeMesh () const

void	SetupSolve (AbstractCellPopulation< DIM, DIM > &rCellPopulation, std::string outputDirectory) override

void	UpdateAtEndOfTimeStep (AbstractCellPopulation< DIM, DIM > &rCellPopulation) override=0

void	UpdateAtEndOfOutputTimeStep (AbstractCellPopulation< DIM, DIM > &rCellPopulation) override

void	UpdateAtEndOfSolve (AbstractCellPopulation< DIM, DIM > &rCellPopulation) override

bool	GetOutputGradient () const

void	SetOutputGradient (bool outputGradient)

void	SetOutputSolutionAtPdeNodes (bool outputSolutionAtPdeNodes)

void	OutputSimulationModifierParameters (out_stream &rParamsFile) override

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

virtual	~AbstractCellBasedSimulationModifier ()

virtual void	UpdateAtEndOfTimeStep (AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > &rCellPopulation)=0

virtual void	UpdateAtEndOfOutputTimeStep (AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > &rCellPopulation)

virtual void	SetupSolve (AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > &rCellPopulation, std::string outputDirectory)=0

virtual void	UpdateAtEndOfSolve (AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > &rCellPopulation)

void	OutputSimulationModifierInfo (out_stream &rParamsFile)

Public Member Functions inherited from Identifiable
virtual	~Identifiable ()

std::string	GetIdentifier () const

Protected Attributes
boost::shared_ptr< AbstractLinearPde< DIM, DIM > >	mpPde

boost::shared_ptr< AbstractBoundaryCondition< DIM > >	mpBoundaryCondition

bool	mIsNeumannBoundaryCondition

std::string	mDependentVariableName

Vec	mSolution = nullptr

TetrahedralMesh< DIM, DIM > *	mpFeMesh = nullptr

std::string	mOutputDirectory {}

bool	mOutputGradient = false

bool	mOutputSolutionAtPdeNodes = false

out_stream	mpVizPdeSolutionResultsFile

bool	mDeleteFeMesh = false

std::vector< double >	mIsDirichletBoundaryNode

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

Friends
class	boost::serialization::access

Detailed Description

template<unsigned DIM>
class AbstractPdeModifier< DIM >

An abstract modifier class containing functionality common to AbstractBoxDomainPdeModifier, AbstractGrowingDomainPdeModifier and their subclasses, which solve a linear elliptic or parabolic PDE coupled to a cell-based simulation.

Definition at line 54 of file AbstractPdeModifier.hpp.

Constructor & Destructor Documentation

◆ AbstractPdeModifier()

template<unsigned DIM>

AbstractPdeModifier< DIM >::AbstractPdeModifier	(	boost::shared_ptr< AbstractLinearPde< DIM, DIM > >	pPde = `NULL`,
		boost::shared_ptr< AbstractBoundaryCondition< DIM > >	pBoundaryCondition = `boost::shared_ptr<AbstractBoundaryCondition<DIM> >()`,
		bool	isNeumannBoundaryCondition = `true`,
		Vec	solution = `nullptr`
	)

Constructor.

Parameters

pPde	A shared pointer to a linear PDE object (defaults to NULL)
pBoundaryCondition	A shared 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	solution vector (defaults to NULL)

Definition at line 44 of file AbstractPdeModifier.cpp.

References AbstractPdeModifier< DIM >::mSolution.

◆ ~AbstractPdeModifier()

template<unsigned DIM>

AbstractPdeModifier< DIM >::~AbstractPdeModifier ( )

override

Destructor.

Definition at line 60 of file AbstractPdeModifier.cpp.

References PetscTools::Destroy().

Member Function Documentation

◆ GetBoundaryCondition()

template<unsigned DIM>

boost::shared_ptr< AbstractBoundaryCondition< DIM > > AbstractPdeModifier< DIM >::GetBoundaryCondition ( )

Returns: mpBoundaryCondition

Definition at line 79 of file AbstractPdeModifier.cpp.

◆ GetFeMesh()

template<unsigned DIM>

TetrahedralMesh< DIM, DIM > * AbstractPdeModifier< DIM >::GetFeMesh ( ) const

Returns: mpFeMesh.

Definition at line 141 of file AbstractPdeModifier.cpp.

◆ GetOutputGradient()

template<unsigned DIM>

bool AbstractPdeModifier< DIM >::GetOutputGradient ( ) const

Set whether to calculate and save the gradient of the solution to CellData.

Returns: mOutputGradient

Definition at line 231 of file AbstractPdeModifier.cpp.

◆ GetPde()

template<unsigned DIM>

boost::shared_ptr< AbstractLinearPde< DIM, DIM > > AbstractPdeModifier< DIM >::GetPde ( )

Returns: mpPde

Definition at line 73 of file AbstractPdeModifier.cpp.

◆ GetSolution() [1/2]

template<unsigned DIM>

Vec AbstractPdeModifier< DIM >::GetSolution ( )

Returns: mSolution.

Definition at line 129 of file AbstractPdeModifier.cpp.

◆ GetSolution() [2/2]

template<unsigned DIM>

Vec AbstractPdeModifier< DIM >::GetSolution ( ) const

Returns: mSolution (used in archiving)

Definition at line 135 of file AbstractPdeModifier.cpp.

◆ HasAveragedSourcePde()

template<unsigned DIM>

bool AbstractPdeModifier< DIM >::HasAveragedSourcePde ( )

Returns: whether the PDE has an averaged source

Definition at line 103 of file AbstractPdeModifier.cpp.

◆ IsNeumannBoundaryCondition()

template<unsigned DIM>

bool AbstractPdeModifier< DIM >::IsNeumannBoundaryCondition ( ) const

Returns: mIsNeumannBoundaryCondition

Definition at line 85 of file AbstractPdeModifier.cpp.

◆ OutputSimulationModifierParameters()

template<unsigned DIM>

void AbstractPdeModifier< DIM >::OutputSimulationModifierParameters ( out_stream & rParamsFile )

overridevirtual

Overridden OutputSimulationModifierParameters() method.

Output any simulation modifier parameters to file.

Parameters

rParamsFile the file stream to which the parameters are output

Implements AbstractCellBasedSimulationModifier< DIM, DIM >.

Reimplemented in ParabolicGrowingDomainPdeModifier< DIM >, EllipticBoxDomainPdeModifier< DIM >, EllipticGrowingDomainPdeModifier< DIM >, and ParabolicBoxDomainPdeModifier< DIM >.

Definition at line 249 of file AbstractPdeModifier.cpp.

References AbstractCellBasedSimulationModifier< ELEMENT_DIM, SPACE_DIM >::OutputSimulationModifierParameters().

Referenced by AbstractBoxDomainPdeModifier< DIM >::OutputSimulationModifierParameters(), and AbstractGrowingDomainPdeModifier< DIM >::OutputSimulationModifierParameters().

◆ rGetDependentVariableName()

template<unsigned DIM>

std::string & AbstractPdeModifier< DIM >::rGetDependentVariableName ( )

Get the name of the dependent variable.

Returns: the name

Definition at line 97 of file AbstractPdeModifier.cpp.

◆ serialize()

template<unsigned DIM>

template<class Archive >

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

inlineprivate

Boost Serialization method for archiving/checkpointing. Archives the object and its member variables.

Parameters

archive	The boost archive.
version	The current version of this class.

Definition at line 68 of file AbstractPdeModifier.hpp.

References AbstractPdeModifier< DIM >::mDependentVariableName, AbstractPdeModifier< DIM >::mIsNeumannBoundaryCondition, AbstractPdeModifier< DIM >::mOutputDirectory, AbstractPdeModifier< DIM >::mOutputGradient, AbstractPdeModifier< DIM >::mOutputSolutionAtPdeNodes, AbstractPdeModifier< DIM >::mpBoundaryCondition, and AbstractPdeModifier< DIM >::mpPde.

◆ SetDependentVariableName()

template<unsigned DIM>

void AbstractPdeModifier< DIM >::SetDependentVariableName ( const std::string & rName )

Set the name of the dependent variable.

Parameters

rName the name.

Definition at line 91 of file AbstractPdeModifier.cpp.

◆ SetOutputGradient()

template<unsigned DIM>

void AbstractPdeModifier< DIM >::SetOutputGradient ( bool outputGradient )

Set whether to calculate and save the gradient of the solution to CellData.

Parameters

outputGradient whether to output the gradient

Definition at line 237 of file AbstractPdeModifier.cpp.

◆ SetOutputSolutionAtPdeNodes()

template<unsigned DIM>

void AbstractPdeModifier< DIM >::SetOutputSolutionAtPdeNodes ( bool outputSolutionAtPdeNodes )

Set mOutputSolutionAtPdeNodes.

Parameters

outputSolutionAtPdeNodes whether to output the PDE solution at each node of the FE mesh at output time steps

Definition at line 243 of file AbstractPdeModifier.cpp.

◆ SetupSolve()

template<unsigned DIM>

void AbstractPdeModifier< DIM >::SetupSolve	(	AbstractCellPopulation< DIM, DIM > &	rCellPopulation,
		std::string	outputDirectory
	)

override

Overridden SetupSolve() method.

Set mOutputDirectory and, if mOutputSolutionAtPdeNodes is set to true, open mpVizPdeSolutionResultsFile. This method is overridden in subclasses.

Parameters

rCellPopulation	reference to the cell population
outputDirectory	the output directory, relative to where Chaste output is stored

Definition at line 147 of file AbstractPdeModifier.cpp.

References PetscTools::AmMaster(), OutputFileHandler::OpenOutputFile(), and AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::Update().

Referenced by ParabolicGrowingDomainPdeModifier< DIM >::SetupSolve(), AbstractBoxDomainPdeModifier< DIM >::SetupSolve(), and EllipticGrowingDomainPdeModifier< DIM >::SetupSolve().

◆ SetUpSourceTermsForAveragedSourcePde()

template<unsigned DIM>

void AbstractPdeModifier< DIM >::SetUpSourceTermsForAveragedSourcePde	(	TetrahedralMesh< DIM, DIM > *	pMesh,
		std::map< CellPtr, unsigned > *	pCellPdeElementMap = `nullptr`
	)

In the case where the PDE has an averaged source, set the source terms using the information in the given mesh.

Parameters

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

Definition at line 111 of file AbstractPdeModifier.cpp.

◆ UpdateAtEndOfOutputTimeStep()

template<unsigned DIM>

void AbstractPdeModifier< DIM >::UpdateAtEndOfOutputTimeStep ( AbstractCellPopulation< DIM, DIM > & rCellPopulation )

override

Overridden UpdateAtEndOfOutputTimeStep() method, after UpdateAtEndOfTimeStep() has been called.

Output the solution to the PDE at each cell to VTK and, if mOutputSolutionAtPdeNodes is set to true, output the solution to the PDE at each node of mpFeMesh to mpVizPdeSolutionResultsFile.

Parameters

rCellPopulation reference to the cell population

Definition at line 166 of file AbstractPdeModifier.cpp.

References PetscTools::AmMaster(), SimulationTime::GetTime(), SimulationTime::GetTimeStepsElapsed(), and SimulationTime::Instance().

◆ UpdateAtEndOfSolve()

template<unsigned DIM>

void AbstractPdeModifier< DIM >::UpdateAtEndOfSolve ( AbstractCellPopulation< DIM, DIM > & rCellPopulation )

override

Overridden UpdateAtEndOfSolve() method.

If mOutputSolutionAtPdeNodes is set to true, close mpVizPdeSolutionResultsFile.

Parameters

rCellPopulation reference to the cell population

Definition at line 219 of file AbstractPdeModifier.cpp.

References PetscTools::AmMaster().

◆ UpdateAtEndOfTimeStep()

template<unsigned DIM>

void AbstractPdeModifier< DIM >::UpdateAtEndOfTimeStep ( AbstractCellPopulation< DIM, DIM > & rCellPopulation )

overridepure virtual

Overridden UpdateAtEndOfTimeStep() method.

As this method is pure virtual, it must be overridden in subclasses.

Parameters

rCellPopulation reference to the cell population

Implemented in ParabolicGrowingDomainPdeModifier< DIM >, EllipticBoxDomainPdeModifier< DIM >, EllipticGrowingDomainPdeModifier< DIM >, and ParabolicBoxDomainPdeModifier< DIM >.

Friends And Related Symbol Documentation

◆ boost::serialization::access

template<unsigned DIM>

friend class boost::serialization::access

friend

Needed for serialization.

Definition at line 59 of file AbstractPdeModifier.hpp.

Member Data Documentation

◆ mDeleteFeMesh

template<unsigned DIM>

bool AbstractPdeModifier< DIM >::mDeleteFeMesh = false

protected

Whether to delete the finite element mesh when we are destroyed.

Definition at line 131 of file AbstractPdeModifier.hpp.

Referenced by AbstractBoxDomainPdeModifier< DIM >::AbstractBoxDomainPdeModifier().

◆ mDependentVariableName

template<unsigned DIM>

std::string AbstractPdeModifier< DIM >::mDependentVariableName

protected

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

Definition at line 105 of file AbstractPdeModifier.hpp.

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

◆ mIsDirichletBoundaryNode

template<unsigned DIM>

std::vector<double> AbstractPdeModifier< DIM >::mIsDirichletBoundaryNode

protected

Store the nodes that dirichlet boundary conditions on which are output with the solution.

Definition at line 136 of file AbstractPdeModifier.hpp.

Referenced by AbstractBoxDomainPdeModifier< DIM >::AbstractBoxDomainPdeModifier().

◆ mIsNeumannBoundaryCondition

template<unsigned DIM>

bool AbstractPdeModifier< DIM >::mIsNeumannBoundaryCondition

protected

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

Todo:: Generalize to allow mixed boundary conditions

Definition at line 99 of file AbstractPdeModifier.hpp.

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

◆ mOutputDirectory

template<unsigned DIM>

std::string AbstractPdeModifier< DIM >::mOutputDirectory {}

protected

Store the output directory name.

Definition at line 114 of file AbstractPdeModifier.hpp.

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

◆ mOutputGradient

template<unsigned DIM>

bool AbstractPdeModifier< DIM >::mOutputGradient = false

protected

Whether to calculate and output the gradient of the solution.

Definition at line 117 of file AbstractPdeModifier.hpp.

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

◆ mOutputSolutionAtPdeNodes

template<unsigned DIM>

bool AbstractPdeModifier< DIM >::mOutputSolutionAtPdeNodes = false

protected

Whether to output the PDE solution at each node of the FE mesh at output time steps. Defaults to false.

Definition at line 123 of file AbstractPdeModifier.hpp.

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

◆ mpBoundaryCondition

template<unsigned DIM>

boost::shared_ptr<AbstractBoundaryCondition<DIM> > AbstractPdeModifier< DIM >::mpBoundaryCondition

protected

Shared pointer to a boundary condition object.

Definition at line 92 of file AbstractPdeModifier.hpp.

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

◆ mpFeMesh

template<unsigned DIM>

TetrahedralMesh<DIM,DIM>* AbstractPdeModifier< DIM >::mpFeMesh = nullptr

protected

Pointer to the finite element mesh on which to solve the PDE.

Definition at line 111 of file AbstractPdeModifier.hpp.

Referenced by AbstractBoxDomainPdeModifier< DIM >::AbstractBoxDomainPdeModifier().

◆ mpPde

template<unsigned DIM>

boost::shared_ptr<AbstractLinearPde<DIM,DIM> > AbstractPdeModifier< DIM >::mpPde

protected

Shared pointer to a linear PDE object.

Definition at line 87 of file AbstractPdeModifier.hpp.

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

◆ mpVizPdeSolutionResultsFile

template<unsigned DIM>

out_stream AbstractPdeModifier< DIM >::mpVizPdeSolutionResultsFile

protected

File that the values of the PDE solution are written out to.

Definition at line 126 of file AbstractPdeModifier.hpp.

◆ mSolution

template<unsigned DIM>

Vec AbstractPdeModifier< DIM >::mSolution = nullptr

protected

The solution to the PDE problem at the current time step.

Definition at line 108 of file AbstractPdeModifier.hpp.

Referenced by AbstractPdeModifier< DIM >::AbstractPdeModifier().

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

cell_based/src/cell_based_pde/AbstractPdeModifier.hpp
cell_based/src/cell_based_pde/AbstractPdeModifier.cpp

Public Member Functions

Protected Attributes

Private Member Functions

Friends

Detailed Description

Constructor & Destructor Documentation

◆ AbstractPdeModifier()

◆ ~AbstractPdeModifier()

Member Function Documentation

◆ GetBoundaryCondition()

◆ GetFeMesh()

◆ GetOutputGradient()

◆ GetPde()

◆ GetSolution() [1/2]

◆ GetSolution() [2/2]

◆ HasAveragedSourcePde()

◆ IsNeumannBoundaryCondition()

◆ OutputSimulationModifierParameters()

◆ rGetDependentVariableName()

◆ serialize()

◆ SetDependentVariableName()

◆ SetOutputGradient()

◆ SetOutputSolutionAtPdeNodes()

◆ SetupSolve()

◆ SetUpSourceTermsForAveragedSourcePde()

◆ UpdateAtEndOfOutputTimeStep()

◆ UpdateAtEndOfSolve()

◆ UpdateAtEndOfTimeStep()

Friends And Related Symbol Documentation

◆ boost::serialization::access

Member Data Documentation

◆ mDeleteFeMesh

◆ mDependentVariableName

◆ mIsDirichletBoundaryNode

◆ mIsNeumannBoundaryCondition

◆ mOutputDirectory

◆ mOutputGradient

◆ mOutputSolutionAtPdeNodes

◆ mpBoundaryCondition

◆ mpFeMesh

◆ mpPde

◆ mpVizPdeSolutionResultsFile

◆ mSolution