#include <CellBasedPdeHandler.hpp>

Inheritance diagram for CellBasedPdeHandler< DIM >:

Collaboration diagram for CellBasedPdeHandler< DIM >:

Public Member Functions
	CellBasedPdeHandler (AbstractCellPopulation< DIM > *pCellPopulation, bool deleteMemberPointersInDestructor=false)

virtual	~CellBasedPdeHandler ()

const AbstractCellPopulation < DIM > *	GetCellPopulation () const

TetrahedralMesh< DIM, DIM > *	GetCoarsePdeMesh ()

void	OpenResultsFiles (std::string outputDirectory)

void	CloseResultsFiles ()

bool	GetWriteAverageRadialPdeSolution ()

bool	GetWriteDailyAverageRadialPdeSolution ()

void	UpdateCellPdeElementMap ()

bool	GetImposeBcsOnCoarseBoundary ()

unsigned	GetNumRadialIntervals ()

virtual void	SolvePdeAndWriteResultsToFile (unsigned samplingTimestepMultiple)

virtual std::auto_ptr < BoundaryConditionsContainer < DIM, DIM, 1 > >	ConstructBoundaryConditionsContainer (PdeAndBoundaryConditions< DIM > pPdeAndBc, TetrahedralMesh< DIM, DIM > pMesh)

double	GetPdeSolutionAtPoint (const c_vector< double, DIM > &rPoint, const std::string &rVariable)

unsigned	FindCoarseElementContainingCell (CellPtr pCell)

virtual Vec	GetPdeSolution (const std::string &rName="")

void	SetWriteAverageRadialPdeSolution (const std::string &rName, unsigned numRadialIntervals=10, bool writeDailyResults=false)

void	SetImposeBcsOnCoarseBoundary (bool setBcsOnCoarseBoundary)

virtual void	UseCoarsePdeMesh (double stepSize, ChasteCuboid< DIM > meshCuboid, bool centreOnCellPopulation=false)

void	AddPdeAndBc (PdeAndBoundaryConditions< DIM > *pPdeAndBc)

virtual void	OutputParameters (out_stream &rParamsFile)

Public Member Functions inherited from Identifiable
virtual	~Identifiable ()

std::string	GetIdentifier () const

Protected Member Functions
void	InitialiseCellPdeElementMap ()

virtual void	WritePdeSolution (double time)

void	WriteAverageRadialPdeSolution (double time)

bool	PdeSolveNeedsCoarseMesh ()

Protected Attributes
AbstractCellPopulation< DIM > *	mpCellPopulation

std::vector < PdeAndBoundaryConditions < DIM > * >	mPdeAndBcCollection

std::string	mDirPath

out_stream	mpVizPdeSolutionResultsFile

out_stream	mpAverageRadialPdeSolutionResultsFile

bool	mWriteAverageRadialPdeSolution

bool	mWriteDailyAverageRadialPdeSolution

std::string	mAverageRadialSolutionVariableName

bool	mSetBcsOnCoarseBoundary

unsigned	mNumRadialIntervals

TetrahedralMesh< DIM, DIM > *	mpCoarsePdeMesh

std::map< CellPtr, unsigned >	mCellPdeElementMap

bool	mDeleteMemberPointersInDestructor

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

Friends
class	TestCellBasedPdeHandler

class	TestOffLatticeSimulationWithPdes

class	TestOnLatticeSimulationWithPdes

class	boost::serialization::access

Detailed Description

template<unsigned DIM>
class CellBasedPdeHandler< DIM >

A helper class, containing code for handling the numerical solution of one or more PDEs (using the finite element method) associated with a cell-based simulation object.

By letting AbstractCellBasedSimulation have a pointer to an object of this type as a member variable, we separate out all PDE-related functionality into this class, and thus obviate the need for specialized cell-based simulation subclasses.

Definition at line 60 of file CellBasedPdeHandler.hpp.

Constructor & Destructor Documentation

template<unsigned DIM>

CellBasedPdeHandler< DIM >::CellBasedPdeHandler	(	AbstractCellPopulation< DIM > *	pCellPopulation,
		bool	deleteMemberPointersInDestructor = `false`
	)

Constructor.

Parameters

pCellPopulation	pointer to a cell population
deleteMemberPointersInDestructor	whether to delete member pointers in the destructor (defaults to false)

Todo:: change to exceptions (#1891)

Definition at line 48 of file CellBasedPdeHandler.cpp.

References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetNumRealCells(), and CellBasedPdeHandler< DIM >::mpCellPopulation.

template<unsigned DIM>

CellBasedPdeHandler< DIM >::~CellBasedPdeHandler ( )

virtual

Destructor.

Definition at line 65 of file CellBasedPdeHandler.cpp.

Member Function Documentation

template<unsigned DIM>

void CellBasedPdeHandler< DIM >::AddPdeAndBc ( PdeAndBoundaryConditions< DIM > * pPdeAndBc )

Pass a PDE and associated boundary conditions to the simulation.

Parameters

pPdeAndBc a pointer to a PdeAndBoundaryConditions object

Definition at line 99 of file CellBasedPdeHandler.cpp.

References EXCEPTION, and PdeAndBoundaryConditions< DIM >::rGetDependentVariableName().

template<unsigned DIM>

void CellBasedPdeHandler< DIM >::CloseResultsFiles ( )

Close results files. Called by AbstractCellBasedSimulation::Solve().

Definition at line 227 of file CellBasedPdeHandler.cpp.

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

template<unsigned DIM>

std::auto_ptr< BoundaryConditionsContainer< DIM, DIM, 1 > > CellBasedPdeHandler< DIM >::ConstructBoundaryConditionsContainer	(	PdeAndBoundaryConditions< DIM > *	pPdeAndBc,
		TetrahedralMesh< DIM, DIM > *	pMesh
	)

virtual

Helper method to construct the boundary conditions container for the PDE.

Parameters

pPdeAndBc	a pointer to the PDE and BCs
pMesh	the mesh on which to solve the PDE

Returns: the full boundary conditions container

Reimplemented in CellBasedPdeHandlerOnCuboid< DIM >.

Definition at line 479 of file CellBasedPdeHandler.cpp.

template<unsigned DIM>

unsigned CellBasedPdeHandler< DIM >::FindCoarseElementContainingCell ( CellPtr pCell )

Find the index of the coarse mesh element containing a given cell.

Parameters

pCell the cell

Returns: the element index.

Definition at line 550 of file CellBasedPdeHandler.cpp.

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

template<unsigned DIM>

const AbstractCellPopulation< DIM > * CellBasedPdeHandler< DIM >::GetCellPopulation ( ) const

Get a pointer to the cell population.

Returns: a const pointer to mpCellPopulation

Definition at line 87 of file CellBasedPdeHandler.cpp.

template<unsigned DIM>

TetrahedralMesh< DIM, DIM > * CellBasedPdeHandler< DIM >::GetCoarsePdeMesh ( )

Returns: mpCoarsePdeMesh

Definition at line 93 of file CellBasedPdeHandler.cpp.

template<unsigned DIM>

bool CellBasedPdeHandler< DIM >::GetImposeBcsOnCoarseBoundary ( )

Returns: mSetBcsOnCoarseBoundary

Definition at line 821 of file CellBasedPdeHandler.cpp.

template<unsigned DIM>

unsigned CellBasedPdeHandler< DIM >::GetNumRadialIntervals ( )

Returns: mNumRadialIntervals

Definition at line 827 of file CellBasedPdeHandler.cpp.

template<unsigned DIM>

Vec CellBasedPdeHandler< DIM >::GetPdeSolution ( const std::string & rName = "" )

virtual

Returns: the solution to the PDE at this time step.

Parameters

rName The name of the dependent variable for the PDE in the vector mPdeAndBcCollection. This defaults to an empty string in the case there is only one PDE.

Definition at line 116 of file CellBasedPdeHandler.cpp.

References EXCEPTION.

template<unsigned DIM>

double CellBasedPdeHandler< DIM >::GetPdeSolutionAtPoint	(	const c_vector< double, DIM > &	rPoint,
		const std::string &	rVariable
	)

Find the solution of one of the PDEs at a point in space

Parameters

rPoint	the position in space
rVariable	the dependent variable of the PDE whose solution you want to find

Returns: the solution of the required PDE at the given point.

Definition at line 750 of file CellBasedPdeHandler.cpp.

References Element< ELEMENT_DIM, SPACE_DIM >::CalculateInterpolationWeights(), EXCEPTION, AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetContainingElementIndex(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetElement(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNodeGlobalIndex(), PdeAndBoundaryConditions< DIM >::GetSolution(), and NEVER_REACHED.

template<unsigned DIM>

bool CellBasedPdeHandler< DIM >::GetWriteAverageRadialPdeSolution ( )

Returns: mWriteAverageRadialPdeSolution

Definition at line 809 of file CellBasedPdeHandler.cpp.

template<unsigned DIM>

bool CellBasedPdeHandler< DIM >::GetWriteDailyAverageRadialPdeSolution ( )

Returns: mWriteDailyAverageRadialPdeSolution

Definition at line 815 of file CellBasedPdeHandler.cpp.

template<unsigned DIM>

void CellBasedPdeHandler< DIM >::InitialiseCellPdeElementMap ( )

protected

Initialise mCellPdeElementMap.

This method is only called Solve(), but is written as a separate method for testing purposes.

Definition at line 138 of file CellBasedPdeHandler.cpp.

References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::Begin(), and EXCEPTION.

template<unsigned DIM>

void CellBasedPdeHandler< DIM >::OpenResultsFiles ( std::string outputDirectory )

Open results files and write initial conditions to file. Called by AbstractCellBasedSimulation::Solve().

Parameters

outputDirectory the output directory, relative to where Chaste output is stored

Definition at line 173 of file CellBasedPdeHandler.cpp.

References PetscTools::AmMaster(), EXCEPTION, ChasteCuboid< SPACE_DIM >::GetWidth(), OutputFileHandler::OpenOutputFile(), and AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFilesUsingMesh().

template<unsigned DIM>

void CellBasedPdeHandler< DIM >::OutputParameters ( out_stream & rParamsFile )

virtual

Output parameters to file.

Parameters

rParamsFile the file stream to which the parameters are output

Reimplemented in CellBasedPdeHandlerOnCuboid< DIM >.

Definition at line 833 of file CellBasedPdeHandler.cpp.

Referenced by CellBasedPdeHandlerOnCuboid< DIM >::OutputParameters().

template<unsigned DIM>

bool CellBasedPdeHandler< DIM >::PdeSolveNeedsCoarseMesh ( )

protected

Returns: Whether the population being used requires the use of separate `coarse` mesh to solve PDEs

Definition at line 846 of file CellBasedPdeHandler.cpp.

template<unsigned DIM>

template<class Archive >

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

inlineprivate

Archive the member variables.

Parameters

archive	the archive
version	the current version of this class

Definition at line 78 of file CellBasedPdeHandler.hpp.

template<unsigned DIM>

void CellBasedPdeHandler< DIM >::SetImposeBcsOnCoarseBoundary ( bool setBcsOnCoarseBoundary )

Impose the PDE boundary conditions on the edge of the cell population when using the coarse mesh. The default option is to impose the condition on the boundary of the coarse mesh.

Parameters

setBcsOnCoarseBoundary whether to impose the BCs on the edge of the cell population

Definition at line 685 of file CellBasedPdeHandler.cpp.

template<unsigned DIM>

void CellBasedPdeHandler< DIM >::SetWriteAverageRadialPdeSolution	(	const std::string &	rName,
		unsigned	numRadialIntervals = `10`,
		bool	writeDailyResults = `false`
	)

Write the final (and optionally also the daily) average radial PDE solution to file.

Parameters

rName	The name of the quantity that we are averaging.
numRadialIntervals	The number of radial intervals in which the average PDE solution is calculated (defaults to 10)
writeDailyResults	Whether to record the average radial PDE solution at the end of each day of the simulation (defaults to false)

Definition at line 676 of file CellBasedPdeHandler.cpp.

template<unsigned DIM>

void CellBasedPdeHandler< DIM >::SolvePdeAndWriteResultsToFile ( unsigned samplingTimestepMultiple )

virtual

Solve the PDE and write the solution to file.

Parameters

samplingTimestepMultiple the ratio of the number of actual timesteps to the number of timesteps at which results are written to file.

Todo:: enable the coarse PDE mesh to change size, e.g. for a growing domain (#630/#1891)

Todo:: enable this in the case where a coarse PDE mesh is used

Todo:: Worry about round-off errors (#1891)

Definition at line 308 of file CellBasedPdeHandler.cpp.

References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::Begin(), Element< ELEMENT_DIM, SPACE_DIM >::CalculateInterpolationWeights(), PetscTools::Destroy(), PdeAndBoundaryConditions< DIM >::DestroySolution(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNodeGlobalIndex(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), PdeAndBoundaryConditions< DIM >::GetPde(), PdeAndBoundaryConditions< DIM >::GetSolution(), SimulationTime::GetTime(), SimulationTime::GetTimeStep(), SimulationTime::GetTimeStepsElapsed(), PdeAndBoundaryConditions< DIM >::HasAveragedSourcePde(), SimulationTime::Instance(), PdeAndBoundaryConditions< DIM >::SetSolution(), and PdeAndBoundaryConditions< DIM >::SetUpSourceTermsForAveragedSourcePde().

template<unsigned DIM>

void CellBasedPdeHandler< DIM >::UpdateCellPdeElementMap ( )

Update the mCellPdeElementMap

This method should be called before sending the element map to a PDE class to ensure map is up to date.

Definition at line 159 of file CellBasedPdeHandler.cpp.

References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::Begin().

template<unsigned DIM>

void CellBasedPdeHandler< DIM >::UseCoarsePdeMesh	(	double	stepSize,
		ChasteCuboid< DIM >	meshCuboid,
		bool	centreOnCellPopulation = `false`
	)

virtual

Solve the PDE problem on a coarse mesh.

Parameters

stepSize	horizontal and vertical distance between mesh points
meshCuboid	the cuboid defining the size and location of the mesh.
centreOnCellPopulation	whether to centre the coarse mesh on the centre of the cell population.

Definition at line 242 of file CellBasedPdeHandler.cpp.

References AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructRegularSlabMesh(), EXCEPTION, ChasteCuboid< SPACE_DIM >::GetWidth(), NEVER_REACHED, ChastePoint< DIM >::rGetLocation(), ChasteCuboid< SPACE_DIM >::rGetLowerCorner(), and ChasteCuboid< SPACE_DIM >::rGetUpperCorner().

template<unsigned DIM>

void CellBasedPdeHandler< DIM >::WriteAverageRadialPdeSolution ( double time )

protected

Write the average radial PDE solution to file at a specified time.

Outputs a line of space-separated values of the form: [time] [radius interval 0] [average solution 0] [radius interval 1] [average solution 1] ...

Parameters

time	The time at which to record the average radial PDE solution

Definition at line 691 of file CellBasedPdeHandler.cpp.

References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::Begin().

template<unsigned DIM>

void CellBasedPdeHandler< DIM >::WritePdeSolution ( double time )

protectedvirtual

Write the PDE solution to file at a specified time.

Outputs a line of space-separated values of the form: [time] [node 0 index] [node 0 x-pos] [node 0 y-pos] [node 0 z-pos] [node 0 solution] ...

where [node 0 index] is equal to 0 if mpCoarsePdeMesh exists, otherwise [node 0 index] is the location index corresponding to the cell first encountered by the cell population Iterator, and so on.

Parameters

time	The time at which to record the PDE solution

Definition at line 582 of file CellBasedPdeHandler.cpp.

References VtkMeshWriter< ELEMENT_DIM, SPACE_DIM >::AddPointData(), PetscTools::AmMaster(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::Begin(), PdeAndBoundaryConditions< DIM >::GetSolution(), SimulationTime::GetTimeStepsElapsed(), SimulationTime::Instance(), NEVER_REACHED, PdeAndBoundaryConditions< DIM >::rGetDependentVariableName(), and VtkMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFilesUsingMesh().

Friends And Related Function Documentation

template<unsigned DIM>

friend class boost::serialization::access

friend

Needed for serialization.

Definition at line 70 of file CellBasedPdeHandler.hpp.

Member Data Documentation

template<unsigned DIM>

std::string CellBasedPdeHandler< DIM >::mAverageRadialSolutionVariableName

protected

The name of the quantity that gets averaged.

Definition at line 112 of file CellBasedPdeHandler.hpp.

Referenced by CellBasedPdeHandler< SPACE_DIM >::serialize().

template<unsigned DIM>

std::map<CellPtr, unsigned> CellBasedPdeHandler< DIM >::mCellPdeElementMap

protected

Map between cells and the elements of the coarse PDE mesh containing them.

Definition at line 124 of file CellBasedPdeHandler.hpp.

template<unsigned DIM>

bool CellBasedPdeHandler< DIM >::mDeleteMemberPointersInDestructor

protected

Whether to delete member pointers in the destructor. Used in archiving.

Definition at line 130 of file CellBasedPdeHandler.hpp.

template<unsigned DIM>

std::string CellBasedPdeHandler< DIM >::mDirPath

protected

A cache of where the results are going (used for VTK writer).

Definition at line 97 of file CellBasedPdeHandler.hpp.

template<unsigned DIM>

unsigned CellBasedPdeHandler< DIM >::mNumRadialIntervals

protected

Number of radial 'bins' used to calculate the average radial PDE solution.

Definition at line 118 of file CellBasedPdeHandler.hpp.

Referenced by CellBasedPdeHandler< SPACE_DIM >::serialize().

template<unsigned DIM>

out_stream CellBasedPdeHandler< DIM >::mpAverageRadialPdeSolutionResultsFile

protected

File that the average radial PDE solution is written out to.

Definition at line 103 of file CellBasedPdeHandler.hpp.

template<unsigned DIM>

AbstractCellPopulation<DIM>* CellBasedPdeHandler< DIM >::mpCellPopulation

protected

Pointer to a cell population.

Definition at line 91 of file CellBasedPdeHandler.hpp.

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

template<unsigned DIM>

TetrahedralMesh<DIM,DIM>* CellBasedPdeHandler< DIM >::mpCoarsePdeMesh

protected

Coarse mesh on which to solve the PDE.

Definition at line 121 of file CellBasedPdeHandler.hpp.

template<unsigned DIM>

std::vector<PdeAndBoundaryConditions<DIM>*> CellBasedPdeHandler< DIM >::mPdeAndBcCollection

protected

Vector of pointers to linear elliptic PDE objects with additional boundary condition information.

Definition at line 94 of file CellBasedPdeHandler.hpp.

Referenced by CellBasedPdeHandler< SPACE_DIM >::serialize().

template<unsigned DIM>

out_stream CellBasedPdeHandler< DIM >::mpVizPdeSolutionResultsFile

protected

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

Definition at line 100 of file CellBasedPdeHandler.hpp.

template<unsigned DIM>

bool CellBasedPdeHandler< DIM >::mSetBcsOnCoarseBoundary

protected

Whether to set the boundary condition on the edge of the coarse mesh rather than the cell population.

Definition at line 115 of file CellBasedPdeHandler.hpp.

Referenced by CellBasedPdeHandler< SPACE_DIM >::serialize().

template<unsigned DIM>

bool CellBasedPdeHandler< DIM >::mWriteAverageRadialPdeSolution

protected

Whether to write to file the average radial PDE solution.

Definition at line 106 of file CellBasedPdeHandler.hpp.

Referenced by CellBasedPdeHandler< SPACE_DIM >::serialize().

template<unsigned DIM>

bool CellBasedPdeHandler< DIM >::mWriteDailyAverageRadialPdeSolution

protected

Whether to write the average radial PDE solution daily.

Definition at line 109 of file CellBasedPdeHandler.hpp.

Referenced by CellBasedPdeHandler< SPACE_DIM >::serialize().

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

cell_based/src/population/pdes/CellBasedPdeHandler.hpp
cell_based/src/population/pdes/CellBasedPdeHandler.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Private Member Functions

Friends

Detailed Description

template<unsigned DIM> class CellBasedPdeHandler< DIM >

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation

template<unsigned DIM>
class CellBasedPdeHandler< DIM >