VertexBasedCellPopulation< DIM > Class Template Reference

#include <VertexBasedCellPopulation.hpp>

Inheritance diagram for VertexBasedCellPopulation< DIM >:

Collaboration diagram for VertexBasedCellPopulation< DIM >:

List of all members.

Public Member Functions

VertexBasedCellPopulation (MutableVertexMesh< DIM, DIM > &rMesh, std::vector< CellPtr > &rCells, bool deleteMesh=false, bool validate=true, const std::vector< unsigned > locationIndices=std::vector< unsigned >())

VertexBasedCellPopulation (MutableVertexMesh< DIM, DIM > &rMesh)

virtual ~VertexBasedCellPopulation ()

double GetDampingConstant (unsigned nodeIndex)

MutableVertexMesh< DIM, DIM > & rGetMesh ()

const MutableVertexMesh< DIM,
DIM > & rGetMesh () const

VertexElement< DIM, DIM > * GetElement (unsigned elementIndex)

unsigned GetNumElements ()

unsigned GetNumNodes ()

c_vector< double, DIM > GetLocationOfCellCentre (CellPtr pCell)

Node< DIM > * GetNode (unsigned index)

unsigned AddNode (Node< DIM > *pNewNode)

void UpdateNodeLocations (const std::vector< c_vector< double, DIM > > &rNodeForces, double dt)

void SetNode (unsigned index, ChastePoint< DIM > &rNewLocation)

VertexElement< DIM, DIM > * GetElementCorrespondingToCell (CellPtr pCell)

CellPtr AddCell (CellPtr pNewCell, const c_vector< double, DIM > &rCellDivisionVector, CellPtr pParentCell=CellPtr())

unsigned RemoveDeadCells ()

bool IsCellAssociatedWithADeletedLocation (CellPtr pCell)

void Update (bool hasHadBirthsOrDeaths=true)

void CreateOutputFiles (const std::string &rDirectory, bool cleanOutputDirectory)

void CloseOutputFiles ()

void WriteResultsToFiles ()

void WriteCellVolumeResultsToFile ()

virtual void GenerateCellResultsAndWriteToFiles ()

void OutputCellPopulationParameters (out_stream &rParamsFile)

double GetWidth (const unsigned &rDimension)

Private Member Functions

void WriteVtkResultsToFile ()

template<class Archive>

void serialize (Archive &archive, const unsigned int version)

void Validate ()

Private Attributes

MutableVertexMesh< DIM, DIM > & mrMesh

bool mDeleteMesh

out_stream mpVizElementsFile

out_stream mpT1SwapLocationsFile

out_stream mpT3SwapLocationsFile

out_stream mpCellVolumesFile

Friends

class boost::serialization::access

Detailed Description

template<unsigned DIM>
class VertexBasedCellPopulation< DIM >

A facade class encapsulating a vertex-based cell population.

Contains a group of cells and maintains the associations between CellPtrs and elements in the MutableVertexMesh.

Definition at line 52 of file VertexBasedCellPopulation.hpp.

Constructor & Destructor Documentation

template<unsigned DIM>

VertexBasedCellPopulation< DIM >::VertexBasedCellPopulation	(	MutableVertexMesh< DIM, DIM > &	rMesh,
		std::vector< CellPtr > &	rCells,
		bool	deleteMesh = `false`,
		bool	validate = `true`,
		const std::vector< unsigned >	locationIndices = `std::vector<unsigned>()`
	)			`[inline]`

Create a new cell population facade from a mesh and collection of cells.

There must be precisely one CellPtr for each VertexElement in the mesh.

Parameters:

	rMesh	reference to a
	rCells	reference to a vector of CellPtrs
	deleteMesh	set to true if you want the cell population to free the mesh memory on destruction
	validate	whether to validate the cell population when it is created (defaults to true)
	locationIndices	an optional vector of location indices that correspond to real cells

Todo:: we should be able to do this, but mBoundaryNodes is not used in vertex meshes (#1558)

Definition at line 35 of file VertexBasedCellPopulation.cpp.

References EXCEPTION, AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNodeIteratorBegin(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNodeIteratorEnd(), VertexBasedCellPopulation< DIM >::mrMesh, and VertexBasedCellPopulation< DIM >::Validate().

template<unsigned DIM>

VertexBasedCellPopulation< DIM >::VertexBasedCellPopulation ( MutableVertexMesh< DIM, DIM > & rMesh ) [inline]

Constructor for use by the de-serializer.

Parameters:

rMesh

a vertex mesh.

Definition at line 71 of file VertexBasedCellPopulation.cpp.

References VertexBasedCellPopulation< DIM >::mDeleteMesh.

template<unsigned DIM>

VertexBasedCellPopulation< DIM >::~VertexBasedCellPopulation ( ) [inline, virtual]

Destructor, which frees any memory allocated by the constructor.

Definition at line 79 of file VertexBasedCellPopulation.cpp.

References VertexBasedCellPopulation< DIM >::mDeleteMesh, and VertexBasedCellPopulation< DIM >::mrMesh.

Member Function Documentation

template<unsigned DIM>

void VertexBasedCellPopulation< DIM >::WriteVtkResultsToFile ( ) [inline, private, virtual]

Overridden WriteVtkResultsToFile() method.

Implements AbstractCellPopulation< DIM >.

Definition at line 498 of file VertexBasedCellPopulation.cpp.

template<unsigned DIM>

template<class Archive>

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

Serialize the object and its member variables.

Note that serialization of the mesh and cells is handled by load/save_construct_data.

Note also that member data related to writers is not saved - output must be set up again by the caller after a restart.

Parameters:

	archive	the archive
	version	the current version of this class

Reimplemented from AbstractCellPopulation< DIM >.

Definition at line 95 of file VertexBasedCellPopulation.hpp.

template<unsigned DIM>

void VertexBasedCellPopulation< DIM >::Validate ( ) [inline, private, virtual]

Check the consistency of internal data structures. Each VertexElement must have a CellPtr associated with it.

Implements AbstractCellPopulation< DIM >.

Definition at line 335 of file VertexBasedCellPopulation.cpp.

References AbstractCellPopulation< DIM >::Begin(), AbstractCellPopulation< DIM >::End(), EXCEPTION, AbstractCellPopulation< DIM >::GetLocationIndexUsingCell(), and VertexBasedCellPopulation< DIM >::GetNumElements().

Referenced by VertexBasedCellPopulation< DIM >::Update(), and VertexBasedCellPopulation< DIM >::VertexBasedCellPopulation().

template<unsigned DIM>

double VertexBasedCellPopulation< DIM >::GetDampingConstant ( unsigned nodeIndex ) [inline, virtual]

Overridden GetDampingConstant() method.

Parameters:

nodeIndex

the global index of this node

Returns:: the average damping constant of the cells surrounding the node.

Implements AbstractCellPopulation< DIM >.

Definition at line 89 of file VertexBasedCellPopulation.cpp.

References AbstractCellPopulation< DIM >::GetCellUsingLocationIndex(), AbstractCellPopulation< DIM >::GetDampingConstantMutant(), AbstractCellPopulation< DIM >::GetDampingConstantNormal(), and VertexBasedCellPopulation< DIM >::GetNode().

Referenced by VertexBasedCellPopulation< DIM >::UpdateNodeLocations().

template<unsigned DIM>

MutableVertexMesh< DIM, DIM > & VertexBasedCellPopulation< DIM >::rGetMesh ( ) [inline]

Returns:: reference to mrMesh.

Definition at line 120 of file VertexBasedCellPopulation.cpp.

References VertexBasedCellPopulation< DIM >::mrMesh.

Referenced by VertexCryptBoundaryForce< DIM >::AddForceContribution(), WelikyOsterForce< DIM >::AddForceContribution(), and NagaiHondaForce< DIM >::AddForceContribution().

template<unsigned DIM>

const MutableVertexMesh< DIM, DIM > & VertexBasedCellPopulation< DIM >::rGetMesh ( ) const [inline]

Returns:: const reference to mrMesh (used in archiving).

Definition at line 127 of file VertexBasedCellPopulation.cpp.

References VertexBasedCellPopulation< DIM >::mrMesh.

template<unsigned DIM>

VertexElement< DIM, DIM > * VertexBasedCellPopulation< DIM >::GetElement ( unsigned elementIndex ) [inline]

Get a particular VertexElement.

Parameters:

elementIndex

the global index of the VertexElement

Returns:: a pointer to the VertexElement.

Definition at line 134 of file VertexBasedCellPopulation.cpp.

References VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetElement(), and VertexBasedCellPopulation< DIM >::mrMesh.

Referenced by NagaiHondaForce< DIM >::AddForceContribution(), VertexBasedCellPopulation< DIM >::WriteCellVolumeResultsToFile(), and VertexBasedCellPopulation< DIM >::WriteResultsToFiles().

template<unsigned DIM>

unsigned VertexBasedCellPopulation< DIM >::GetNumElements ( ) [inline]

Returns:: the number of VertexElements in the cell population.

Definition at line 183 of file VertexBasedCellPopulation.cpp.

References MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::GetNumElements(), and VertexBasedCellPopulation< DIM >::mrMesh.

Referenced by VertexBasedCellPopulation< DIM >::Validate().

template<unsigned DIM>

unsigned VertexBasedCellPopulation< DIM >::GetNumNodes ( ) [inline, virtual]

Overridden GetNumNodes() method.

Returns:: the number of nodes in the cell population.

Implements AbstractCellPopulation< DIM >.

Definition at line 141 of file VertexBasedCellPopulation.cpp.

References MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), and VertexBasedCellPopulation< DIM >::mrMesh.

Referenced by NagaiHondaForce< DIM >::AddForceContribution(), and VertexBasedCellPopulation< DIM >::UpdateNodeLocations().

template<unsigned DIM>

c_vector< double, DIM > VertexBasedCellPopulation< DIM >::GetLocationOfCellCentre ( CellPtr pCell ) [inline, virtual]

Overridden GetLocationOfCellCentre() method. Find where a given cell is in space.

Todo:: If required, we could come up with a more clever definition of cell location for a VertexCellPopulation (for example, there is no guarantee of convexity so the centre of mass may lie outside the element)

Parameters:

pCell

the cell

Returns:: the location of the centre of mass of the element corresponding to this cell.

Implements AbstractCellPopulation< DIM >.

Definition at line 148 of file VertexBasedCellPopulation.cpp.

References VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetCentroidOfElement(), AbstractCellPopulation< DIM >::mCellLocationMap, and VertexBasedCellPopulation< DIM >::mrMesh.

Referenced by VertexBasedCellPopulation< DIM >::WriteCellVolumeResultsToFile().

template<unsigned DIM>

Node< DIM > * VertexBasedCellPopulation< DIM >::GetNode ( unsigned index ) [inline, virtual]

Overridden GetNode() method.

Parameters:

index

global index of the specified node

Returns:: a pointer to the node.

Implements AbstractCellPopulation< DIM >.

Definition at line 155 of file VertexBasedCellPopulation.cpp.

References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNode(), and VertexBasedCellPopulation< DIM >::mrMesh.

Referenced by NagaiHondaForce< DIM >::AddForceContribution(), VertexBasedCellPopulation< DIM >::GetDampingConstant(), and VertexBasedCellPopulation< DIM >::UpdateNodeLocations().

template<unsigned DIM>

unsigned VertexBasedCellPopulation< DIM >::AddNode ( Node< DIM > * pNewNode ) [inline, virtual]

Overridden AddNode() method.

Add a new node to the cell population.

Parameters:

pNewNode

pointer to the new node

Returns:: global index of new node in cell population

Implements AbstractCellPopulation< DIM >.

Definition at line 162 of file VertexBasedCellPopulation.cpp.

References MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::AddNode(), and VertexBasedCellPopulation< DIM >::mrMesh.

template<unsigned DIM>

void VertexBasedCellPopulation< DIM >::UpdateNodeLocations	(	const std::vector< c_vector< double, DIM > > &	rNodeForces,
		double	dt
	)			`[inline, virtual]`

Overridden UpdateNodeLocations() method.

Parameters:

	rNodeForces	a vector containing the force on each node in the cell population
	dt	the time step

Implements AbstractCellPopulation< DIM >.

Definition at line 242 of file VertexBasedCellPopulation.cpp.

References MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::GetCellRearrangementThreshold(), VertexBasedCellPopulation< DIM >::GetDampingConstant(), VertexBasedCellPopulation< DIM >::GetNode(), VertexBasedCellPopulation< DIM >::GetNumNodes(), VertexBasedCellPopulation< DIM >::mrMesh, and VertexBasedCellPopulation< DIM >::SetNode().

template<unsigned DIM>

void VertexBasedCellPopulation< DIM >::SetNode	(	unsigned	index,
		ChastePoint< DIM > &	rNewLocation
	)			`[inline, virtual]`

Overridden SetNode() method.

Move the node with a given index to a new point in space.

Parameters:

	index	the index of the node to be moved
	rNewLocation	the new target location of the node

Implements AbstractCellPopulation< DIM >.

Definition at line 169 of file VertexBasedCellPopulation.cpp.

References VertexBasedCellPopulation< DIM >::mrMesh, and MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::SetNode().

Referenced by VertexBasedCellPopulation< DIM >::UpdateNodeLocations().

template<unsigned DIM>

VertexElement< DIM, DIM > * VertexBasedCellPopulation< DIM >::GetElementCorrespondingToCell ( CellPtr pCell ) [inline]

Get a pointer to the element corresponding to a given CellPtr.

Parameters:

pCell

the cell

Returns:: pointer to the element.

Definition at line 176 of file VertexBasedCellPopulation.cpp.

References VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetElement(), AbstractCellPopulation< DIM >::mCellLocationMap, and VertexBasedCellPopulation< DIM >::mrMesh.

Referenced by VertexBasedCellPopulation< DIM >::AddCell(), and VertexBasedCellPopulation< DIM >::IsCellAssociatedWithADeletedLocation().

template<unsigned DIM>

CellPtr VertexBasedCellPopulation< DIM >::AddCell	(	CellPtr	pNewCell,
		const c_vector< double, DIM > &	rCellDivisionVector,
		CellPtr	pParentCell = `CellPtr()`
	)			`[inline, virtual]`

Overridden AddCell() method.

Add a new cell to the cell population.

Parameters:

	pNewCell	the cell to add
	rCellDivisionVector	if this vector has any non-zero component, then it is used as the axis along which the parent cell divides
	pParentCell	pointer to a parent cell (if required)

Returns:: address of cell as it appears in the cell list (internal of this method uses a copy constructor along the way)

Implements AbstractCellPopulation< DIM >.

Definition at line 190 of file VertexBasedCellPopulation.cpp.

References MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::DivideElementAlongGivenAxis(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::DivideElementAlongShortAxis(), VertexBasedCellPopulation< DIM >::GetElementCorrespondingToCell(), AbstractCellPopulation< DIM >::mCellLocationMap, AbstractCellPopulation< DIM >::mCells, AbstractCellPopulation< DIM >::mLocationCellMap, and VertexBasedCellPopulation< DIM >::mrMesh.

template<unsigned DIM>

unsigned VertexBasedCellPopulation< DIM >::RemoveDeadCells ( ) [inline, virtual]

Remove all cells labelled as dead.

Note that after calling this method the cell population will be in an inconsistent state until the equivalent of a 'remesh' is performed! So don't try iterating over cells or anything like that.

Returns:: number of cells removed

Implements AbstractCellPopulation< DIM >.

Definition at line 220 of file VertexBasedCellPopulation.cpp.

References MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::DeleteElementPriorToReMesh(), AbstractCellPopulation< DIM >::mCellLocationMap, AbstractCellPopulation< DIM >::mCells, and VertexBasedCellPopulation< DIM >::mrMesh.

template<unsigned DIM>

bool VertexBasedCellPopulation< DIM >::IsCellAssociatedWithADeletedLocation ( CellPtr pCell ) [inline, virtual]

Overridden IsCellAssociatedWithADeletedLocation() method.

Parameters:

pCell

the cell

Returns:: whether a given cell is associated with a deleted element.

Implements AbstractCellPopulation< DIM >.

Definition at line 279 of file VertexBasedCellPopulation.cpp.

References VertexBasedCellPopulation< DIM >::GetElementCorrespondingToCell().

template<unsigned DIM>

void VertexBasedCellPopulation< DIM >::Update ( bool hasHadBirthsOrDeaths = true ) [inline, virtual]

Remove the VertexElements which have been marked as deleted, perform any cell rearrangements if required, and update the correspondence with CellPtrs.

Parameters:

hasHadBirthsOrDeaths

- a bool saying whether cell population has had Births Or Deaths not needed in this cell population class

Todo:: this is a kludge to remove the cell once a T2Swap occurs this is not included in the dead cells counter. This should be included in the RemoveDeadCells method so the death is counted

Implements AbstractCellPopulation< DIM >.

Definition at line 286 of file VertexBasedCellPopulation.cpp.

References VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetNumAllElements(), AbstractCellPopulation< DIM >::mCellLocationMap, AbstractCellPopulation< DIM >::mCells, AbstractCellPopulation< DIM >::mLocationCellMap, VertexBasedCellPopulation< DIM >::mrMesh, MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::ReMesh(), and VertexBasedCellPopulation< DIM >::Validate().

template<unsigned DIM>

void VertexBasedCellPopulation< DIM >::CreateOutputFiles	(	const std::string &	rDirectory,
		bool	cleanOutputDirectory
	)			`[inline, virtual]`

Overridden CreateOutputFiles() method.

Parameters:

	rDirectory	pathname of the output directory, relative to where Chaste output is stored
	cleanOutputDirectory	whether to delete the contents of the output directory prior to output file creation

Reimplemented from AbstractCellPopulation< DIM >.

Definition at line 626 of file VertexBasedCellPopulation.cpp.

References AbstractCellPopulation< DIM >::CreateOutputFiles(), AbstractCellPopulation< DIM >::mOutputCellVolumes, VertexBasedCellPopulation< DIM >::mpCellVolumesFile, VertexBasedCellPopulation< DIM >::mpT1SwapLocationsFile, VertexBasedCellPopulation< DIM >::mpT3SwapLocationsFile, VertexBasedCellPopulation< DIM >::mpVizElementsFile, and OutputFileHandler::OpenOutputFile().

template<unsigned DIM>

void VertexBasedCellPopulation< DIM >::CloseOutputFiles ( ) [inline, virtual]

Overridden CloseOutputFiles() method.

Reimplemented from AbstractCellPopulation< DIM >.

Definition at line 642 of file VertexBasedCellPopulation.cpp.

References AbstractCellPopulation< DIM >::CloseOutputFiles(), AbstractCellPopulation< DIM >::mOutputCellVolumes, VertexBasedCellPopulation< DIM >::mpCellVolumesFile, VertexBasedCellPopulation< DIM >::mpT1SwapLocationsFile, VertexBasedCellPopulation< DIM >::mpT3SwapLocationsFile, and VertexBasedCellPopulation< DIM >::mpVizElementsFile.

template<unsigned DIM>

void VertexBasedCellPopulation< DIM >::WriteResultsToFiles ( ) [inline, virtual]

Overridden WriteResultsToFiles() method.

Reimplemented from AbstractCellPopulation< DIM >.

Definition at line 368 of file VertexBasedCellPopulation.cpp.

References MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::ClearLocationsOfT1Swaps(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::ClearLocationsOfT3Swaps(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetElement(), VertexBasedCellPopulation< DIM >::GetElement(), AbstractCellPopulation< DIM >::GetLocationIndexUsingCell(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::GetLocationsOfT1Swaps(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::GetLocationsOfT3Swaps(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNodeGlobalIndex(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), SimulationTime::GetTime(), SimulationTime::Instance(), AbstractCellPopulation< DIM >::mCells, AbstractCellPopulation< DIM >::mLocationCellMap, AbstractCellPopulation< DIM >::mOutputCellVolumes, VertexBasedCellPopulation< DIM >::mpT1SwapLocationsFile, VertexBasedCellPopulation< DIM >::mpT3SwapLocationsFile, VertexBasedCellPopulation< DIM >::mpVizElementsFile, VertexBasedCellPopulation< DIM >::mrMesh, VertexBasedCellPopulation< DIM >::WriteCellVolumeResultsToFile(), and AbstractCellPopulation< DIM >::WriteResultsToFiles().

template<unsigned DIM>

void VertexBasedCellPopulation< DIM >::WriteCellVolumeResultsToFile ( ) [inline]

Write the current index and location (of the centre) of each element in mrMesh, as well as the ID and the area (in 2D) or volume (in 3D) of its corresponding cell, to mpCellVolumesFile.

Definition at line 448 of file VertexBasedCellPopulation.cpp.

References VertexBasedCellPopulation< DIM >::GetElement(), AbstractCellPopulation< DIM >::GetLocationIndexUsingCell(), VertexBasedCellPopulation< DIM >::GetLocationOfCellCentre(), SimulationTime::GetTime(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetVolumeOfElement(), SimulationTime::Instance(), AbstractCellPopulation< DIM >::mCells, AbstractCellPopulation< DIM >::mLocationCellMap, VertexBasedCellPopulation< DIM >::mpCellVolumesFile, and VertexBasedCellPopulation< DIM >::mrMesh.

Referenced by VertexBasedCellPopulation< DIM >::WriteResultsToFiles().

template<unsigned DIM>

void VertexBasedCellPopulation< DIM >::GenerateCellResultsAndWriteToFiles ( ) [inline, virtual]

Overridden GenerateCellResultsAndWriteToFiles() method.

Implements AbstractCellPopulation< DIM >.

Definition at line 657 of file VertexBasedCellPopulation.cpp.

References AbstractCellPopulation< DIM >::Begin(), AbstractCellPopulation< DIM >::End(), AbstractCellPopulation< DIM >::GenerateCellResults(), AbstractCellPopulation< DIM >::GetLocationIndexUsingCell(), AbstractCellPopulation< DIM >::mCellCyclePhaseCount, AbstractCellPopulation< DIM >::mCellProliferativeTypeCount, and AbstractCellPopulation< DIM >::WriteCellResultsToFiles().

template<unsigned DIM>

void VertexBasedCellPopulation< DIM >::OutputCellPopulationParameters ( out_stream & rParamsFile ) [inline, virtual]

Outputs CellPopulation parameters to file

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

Parameters:

rParamsFile

the file stream to which the parameters are output

Implements AbstractCellPopulation< DIM >.

Definition at line 686 of file VertexBasedCellPopulation.cpp.

References MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::GetCellRearrangementRatio(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::GetCellRearrangementThreshold(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::GetT2Threshold(), VertexBasedCellPopulation< DIM >::mrMesh, and AbstractCellPopulation< DIM >::OutputCellPopulationParameters().

template<unsigned DIM>

double VertexBasedCellPopulation< DIM >::GetWidth ( const unsigned & rDimension ) [inline, virtual]

Overridden GetWidth() method.

Calculate the 'width' of any dimension of the cell population by calling GetWidth() on the mesh.

Parameters:

rDimension

a dimension (0,1 or 2)

Returns:: The maximum distance between any nodes in this dimension.

Implements AbstractCellPopulation< DIM >.

Definition at line 697 of file VertexBasedCellPopulation.cpp.

References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetWidth(), and VertexBasedCellPopulation< DIM >::mrMesh.

Friends And Related Function Documentation

template<unsigned DIM>

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

Needed for serialization.

Reimplemented from AbstractCellPopulation< DIM >.

Definition at line 82 of file VertexBasedCellPopulation.hpp.

Member Data Documentation

template<unsigned DIM>

MutableVertexMesh<DIM, DIM>& VertexBasedCellPopulation< DIM >::mrMesh [private]

Vertex-based mesh associated with the cell population.

Definition at line 57 of file VertexBasedCellPopulation.hpp.

template<unsigned DIM>

bool VertexBasedCellPopulation< DIM >::mDeleteMesh [private]

Whether to delete the mesh when we are destroyed. Needed if this cell population has been de-serialized.

Definition at line 63 of file VertexBasedCellPopulation.hpp.

Referenced by VertexBasedCellPopulation< DIM >::VertexBasedCellPopulation(), and VertexBasedCellPopulation< DIM >::~VertexBasedCellPopulation().

template<unsigned DIM>

out_stream VertexBasedCellPopulation< DIM >::mpVizElementsFile [private]

Results file for elements.

Definition at line 66 of file VertexBasedCellPopulation.hpp.

Referenced by VertexBasedCellPopulation< DIM >::CloseOutputFiles(), VertexBasedCellPopulation< DIM >::CreateOutputFiles(), and VertexBasedCellPopulation< DIM >::WriteResultsToFiles().

template<unsigned DIM>

out_stream VertexBasedCellPopulation< DIM >::mpT1SwapLocationsFile [private]

Results file for locations of T1Swaps.

Definition at line 69 of file VertexBasedCellPopulation.hpp.

Referenced by VertexBasedCellPopulation< DIM >::CloseOutputFiles(), VertexBasedCellPopulation< DIM >::CreateOutputFiles(), and VertexBasedCellPopulation< DIM >::WriteResultsToFiles().

template<unsigned DIM>

out_stream VertexBasedCellPopulation< DIM >::mpT3SwapLocationsFile [private]

Results file for locations of T3Swaps.

Definition at line 72 of file VertexBasedCellPopulation.hpp.

Referenced by VertexBasedCellPopulation< DIM >::CloseOutputFiles(), VertexBasedCellPopulation< DIM >::CreateOutputFiles(), and VertexBasedCellPopulation< DIM >::WriteResultsToFiles().

template<unsigned DIM>

out_stream VertexBasedCellPopulation< DIM >::mpCellVolumesFile [private]

Results file for cell volume (in 3D) or area (in 2D) data.

Definition at line 75 of file VertexBasedCellPopulation.hpp.

Referenced by VertexBasedCellPopulation< DIM >::CloseOutputFiles(), VertexBasedCellPopulation< DIM >::CreateOutputFiles(), and VertexBasedCellPopulation< DIM >::WriteCellVolumeResultsToFile().

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

cell_based/src/population/VertexBasedCellPopulation.hpp
cell_based/src/population/VertexBasedCellPopulation.cpp


Public Member Functions
	VertexBasedCellPopulation (MutableVertexMesh< DIM, DIM > &rMesh, std::vector< CellPtr > &rCells, bool deleteMesh=false, bool validate=true, const std::vector< unsigned > locationIndices=std::vector< unsigned >())
	VertexBasedCellPopulation (MutableVertexMesh< DIM, DIM > &rMesh)
virtual	~VertexBasedCellPopulation ()
double	GetDampingConstant (unsigned nodeIndex)
MutableVertexMesh< DIM, DIM > &	rGetMesh ()
const MutableVertexMesh< DIM, DIM > &	rGetMesh () const
VertexElement< DIM, DIM > *	GetElement (unsigned elementIndex)
unsigned	GetNumElements ()
unsigned	GetNumNodes ()
c_vector< double, DIM >	GetLocationOfCellCentre (CellPtr pCell)
Node< DIM > *	GetNode (unsigned index)
unsigned	AddNode (Node< DIM > *pNewNode)
void	UpdateNodeLocations (const std::vector< c_vector< double, DIM > > &rNodeForces, double dt)
void	SetNode (unsigned index, ChastePoint< DIM > &rNewLocation)
VertexElement< DIM, DIM > *	GetElementCorrespondingToCell (CellPtr pCell)
CellPtr	AddCell (CellPtr pNewCell, const c_vector< double, DIM > &rCellDivisionVector, CellPtr pParentCell=CellPtr())
unsigned	RemoveDeadCells ()
bool	IsCellAssociatedWithADeletedLocation (CellPtr pCell)
void	Update (bool hasHadBirthsOrDeaths=true)
void	CreateOutputFiles (const std::string &rDirectory, bool cleanOutputDirectory)
void	CloseOutputFiles ()
void	WriteResultsToFiles ()
void	WriteCellVolumeResultsToFile ()
virtual void	GenerateCellResultsAndWriteToFiles ()
void	OutputCellPopulationParameters (out_stream &rParamsFile)
double	GetWidth (const unsigned &rDimension)
Private Member Functions
void	WriteVtkResultsToFile ()
template<class Archive>
void	serialize (Archive &archive, const unsigned int version)
void	Validate ()
Private Attributes
MutableVertexMesh< DIM, DIM > &	mrMesh
bool	mDeleteMesh
out_stream	mpVizElementsFile
out_stream	mpT1SwapLocationsFile
out_stream	mpT3SwapLocationsFile
out_stream	mpCellVolumesFile
Friends
class	boost::serialization::access

VertexBasedCellPopulation< DIM > Class Template Reference

Public Member Functions

Private Member Functions

Private Attributes

Friends

Detailed Description

template<unsigned DIM> class VertexBasedCellPopulation< DIM >

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation

template<unsigned DIM>
class VertexBasedCellPopulation< DIM >