MeshBasedTissue< DIM > Class Template Reference

#include <MeshBasedTissue.hpp>

Inherits AbstractCellCentreBasedTissue< DIM >.

Inherited by MeshBasedTissueWithGhostNodes< DIM >, and MeshBasedTissueWithGhostNodes< 2 >.

Collaboration diagram for MeshBasedTissue< DIM >:

Classes
class	SpringIterator
Public Member Functions
	MeshBasedTissue (MutableMesh< DIM, DIM > &rMesh, std::vector< TissueCell > &rCells, const std::vector< unsigned > locationIndices=std::vector< unsigned >(), bool deleteMesh=false, bool validate=true)
	MeshBasedTissue (MutableMesh< DIM, DIM > &rMesh)
	~MeshBasedTissue ()
MutableMesh< DIM, DIM > &	rGetMesh ()
const MutableMesh< DIM, DIM > &	rGetMesh () const
bool	UseAreaBasedDampingConstant ()
void	SetOutputVoronoiData (bool writeVoronoiData)
unsigned	AddNode (Node< DIM > *pNewNode)
void	SetNode (unsigned nodeIndex, ChastePoint< DIM > &rNewLocation)
double	GetDampingConstant (unsigned nodeIndex)
void	SetOutputTissueAreas (bool writeTissueAreas)
void	SetAreaBasedDampingConstant (bool useAreaBasedDampingConstant)
virtual unsigned	RemoveDeadCells ()
virtual TissueCell *	AddCell (TissueCell &rNewCell, const c_vector< double, DIM > &rCellDivisionVector, TissueCell *pParentCell=NULL)
void	CreateOutputFiles (const std::string &rDirectory, bool cleanOutputDirectory)
void	CloseOutputFiles ()
void	WriteResultsToFiles ()
virtual void	Update (bool hasHadBirthsOrDeaths=true)
Node< DIM > *	GetNode (unsigned index)
unsigned	GetNumNodes ()
void	WriteVoronoiResultsToFile ()
void	WriteTissueAreaResultsToFile ()
void	WriteCellAreaResultsToFile ()
void	CreateVoronoiTessellation (const std::vector< unsigned > locationIndices=std::vector< unsigned >())
VoronoiTessellation< DIM > &	rGetVoronoiTessellation ()
SpringIterator	SpringsBegin ()
SpringIterator	SpringsEnd ()
void	CheckTissueCellPointers ()
std::set< TissueCell * >	CreateCellPair (TissueCell &rCell1, TissueCell &rCell2)
bool	IsMarkedSpring (const std::set< TissueCell * > &rCellPair)
void	MarkSpring (std::set< TissueCell * > &rCellPair)
void	UnmarkSpring (std::set< TissueCell * > &rCellPair)
Protected Member Functions
virtual void	UpdateGhostNodesAfterReMesh (NodeMap &rMap)
virtual void	Validate ()
Protected Attributes
MutableMesh< DIM, DIM > &	mrMesh
VoronoiTessellation< DIM > *	mpVoronoiTessellation
bool	mDeleteMesh
std::set< std::set< TissueCell * > >	mMarkedSprings
out_stream	mpElementFile
out_stream	mpVoronoiFile
out_stream	mpTissueAreasFile
out_stream	mpCellAreasFile
bool	mUseAreaBasedDampingConstant
Private Member Functions
template<class Archive >
void	serialize (Archive &archive, const unsigned int version)
Friends
class	TestMeshBasedTissue
class	boost::serialization::access

Detailed Description

template<unsigned DIM>
class MeshBasedTissue< DIM >

A facade class encapsulating a mesh-based 'tissue'

Contains a group of cells and maintains the associations between cells and nodes in the mesh.

Definition at line 52 of file MeshBasedTissue.hpp.

Constructor & Destructor Documentation

template<unsigned DIM>

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

Create a new tissue facade from a mesh and collection of cells.

There must be precisely 1 cell for each node of the mesh.

Parameters:

	rMesh	a mutable tetrahedral mesh
	rCells	TissueCells corresponding to the nodes of the mesh
	locationIndices	an optional vector of location indices that correspond to real cells
	deleteMesh	set to true if you want the tissue to free the mesh memory on destruction
	validate	whether to validate the tissue

Definition at line 33 of file MeshBasedTissue.cpp.

References MutableMesh< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), AbstractTissue< DIM >::mCells, MeshBasedTissue< DIM >::mrMesh, AbstractTissue< DIM >::mTissueContainsMesh, and MeshBasedTissue< DIM >::Validate().

template<unsigned DIM>

MeshBasedTissue< DIM >::MeshBasedTissue ( MutableMesh< DIM, DIM > & rMesh ) [inline]

Constructor for use by the de-serializer.

Parameters:

rMesh

a mutable tetrahedral mesh.

Definition at line 56 of file MeshBasedTissue.cpp.

References MeshBasedTissue< DIM >::mDeleteMesh, MeshBasedTissue< DIM >::mpVoronoiTessellation, and AbstractTissue< DIM >::mTissueContainsMesh.

template<unsigned DIM>

MeshBasedTissue< DIM >::~MeshBasedTissue ( ) [inline]

Destructor.

Definition at line 65 of file MeshBasedTissue.cpp.

References MeshBasedTissue< DIM >::mDeleteMesh, MeshBasedTissue< DIM >::mpVoronoiTessellation, and MeshBasedTissue< DIM >::mrMesh.

Member Function Documentation

template<unsigned DIM>

TissueCell * MeshBasedTissue< DIM >::AddCell	(	TissueCell &	rNewCell,
		const c_vector< double, DIM > &	rCellDivisionVector,
		TissueCell *	pParentCell = `NULL`
	)			`[inline, virtual]`

Overridden AddCell() method.

Add a new cell to the tissue and update mIsGhostNode.

Parameters:

	rNewCell	the cell to add
	rCellDivisionVector	the position in space at which to put it
	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)

Reimplemented from AbstractCellCentreBasedTissue< DIM >.

Reimplemented in MeshBasedTissueWithGhostNodes< DIM >, and MeshBasedTissueWithGhostNodes< 2 >.

Definition at line 354 of file MeshBasedTissue.cpp.

References MeshBasedTissue< DIM >::CreateCellPair(), and MeshBasedTissue< DIM >::MarkSpring().

template<unsigned DIM>

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

Overridden AddNode() method.

Add a new node to the tissue.

Parameters:

pNewNode

pointer to the new node

Returns:: global index of new node in tissue

Implements AbstractTissue< DIM >.

Definition at line 90 of file MeshBasedTissue.cpp.

References MutableMesh< ELEMENT_DIM, SPACE_DIM >::AddNode(), and MeshBasedTissue< DIM >::mrMesh.

template<unsigned DIM>

void MeshBasedTissue< DIM >::CheckTissueCellPointers ( ) [inline]

Helper method for use in debugging.

Definition at line 697 of file MeshBasedTissue.cpp.

References AbstractCellCycleModel::GetCell(), TissueCell::GetCellCycleModel(), TissueCell::IsDead(), AbstractTissue< DIM >::mCellLocationMap, AbstractTissue< DIM >::mCells, MeshBasedTissue< DIM >::mMarkedSprings, and AbstractTissue< DIM >::rGetCellUsingLocationIndex().

template<unsigned DIM>

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

Overridden CloseOutputFiles() method.

Reimplemented from AbstractTissue< DIM >.

Definition at line 395 of file MeshBasedTissue.cpp.

References TissueConfig::Instance(), MeshBasedTissue< DIM >::mpCellAreasFile, MeshBasedTissue< DIM >::mpElementFile, MeshBasedTissue< DIM >::mpTissueAreasFile, and MeshBasedTissue< DIM >::mpVoronoiFile.

template<unsigned DIM>

std::set< TissueCell * > MeshBasedTissue< DIM >::CreateCellPair	(	TissueCell &	rCell1,
		TissueCell &	rCell2
	)			`[inline]`

Helper method that returns a set of pointers to two given TissueCells. Used by the spring marking routines.

Parameters:

	rCell1	a TissueCell
	rCell2	a TissueCell

Definition at line 777 of file MeshBasedTissue.cpp.

Referenced by MeshBasedTissue< DIM >::AddCell(), and GeneralisedLinearSpringForce< DIM >::CalculateForceBetweenNodes().

template<unsigned DIM>

void MeshBasedTissue< 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 AbstractTissue< DIM >.

Definition at line 373 of file MeshBasedTissue.cpp.

References TissueConfig::Instance(), MeshBasedTissue< DIM >::mpCellAreasFile, MeshBasedTissue< DIM >::mpElementFile, MeshBasedTissue< DIM >::mpTissueAreasFile, MeshBasedTissue< DIM >::mpVoronoiFile, and OutputFileHandler::OpenOutputFile().

template<unsigned DIM>

void MeshBasedTissue< DIM >::CreateVoronoiTessellation ( const std::vector< unsigned > locationIndices = std::vector<unsigned>() ) [inline]

Get a reference to a Voronoi tessellation of the mesh.

Parameters:

locationIndices

an optional vector of location indices that correspond to non-ghost nodes

Definition at line 672 of file MeshBasedTissue.cpp.

References MeshBasedTissue< DIM >::mpVoronoiTessellation, and MeshBasedTissue< DIM >::mrMesh.

Referenced by MeshBasedTissue< DIM >::Update().

template<unsigned DIM>

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

Overridden GetDampingConstant() method that includes the case of a cell-area-based damping constant.

Parameters:

nodeIndex

the global index of this node

Returns:: the damping constant for the given TissueCell.

We use a linear dependence of the form

new_damping_const = old_damping_const * (d0+d1*A)

where d0, d1 are parameters, A is the cell's area, and old_damping_const is the damping constant if not using mUseAreaBasedDampingConstant

Compute the parameter d1 such that d0+A*d1=1, where A is the equilibrium area of a cell (this is equal to sqrt(3)/4, which is a third of the area of a regular hexagon of edge length 1)

The cell area should not be too large - the next assertion is to avoid getting an infinite cell area, which may occur if area-based viscosity is chosen in the absence of ghost nodes.

Reimplemented from AbstractCellCentreBasedTissue< DIM >.

Definition at line 102 of file MeshBasedTissue.cpp.

References TissueConfig::GetAreaBasedDampingConstantParameter(), VoronoiTessellation< DIM >::GetFaceArea(), TissueConfig::Instance(), MeshBasedTissue< DIM >::mUseAreaBasedDampingConstant, and MeshBasedTissue< DIM >::rGetVoronoiTessellation().

template<unsigned DIM>

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

Overridden GetNode() method.

Parameters:

index

global index of the specified Node

Returns:: pointer to the Node with given index.

Implements AbstractTissue< DIM >.

Definition at line 337 of file MeshBasedTissue.cpp.

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

Referenced by MeshBasedTissueWithGhostNodes< DIM >::CalculateForceBetweenNodes(), MeshBasedTissueWithGhostNodes< DIM >::MeshBasedTissueWithGhostNodes(), and MeshBasedTissue< DIM >::WriteResultsToFiles().

template<unsigned DIM>

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

Overridden GetNumNodes() method.

Returns:: the number of nodes in the tissue.

Implements AbstractTissue< DIM >.

Definition at line 343 of file MeshBasedTissue.cpp.

References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNumAllNodes(), and MeshBasedTissue< DIM >::mrMesh.

Referenced by MeshBasedTissueWithGhostNodes< DIM >::AddCell(), MeshBasedTissueWithGhostNodes< DIM >::MeshBasedTissueWithGhostNodes(), MeshBasedTissueWithGhostNodes< DIM >::UpdateGhostNodesAfterReMesh(), MeshBasedTissueWithGhostNodes< DIM >::UpdateGhostPositions(), MeshBasedTissueWithGhostNodes< DIM >::Validate(), and MeshBasedTissue< DIM >::Validate().

template<unsigned DIM>

bool MeshBasedTissue< DIM >::IsMarkedSpring ( const std::set< TissueCell * > & rCellPair ) [inline]

Parameters:

rCellPair

a set of pointers to TissueCells

Returns:: whether the spring between two given cells is marked.

Definition at line 786 of file MeshBasedTissue.cpp.

References MeshBasedTissue< DIM >::mMarkedSprings.

Referenced by GeneralisedLinearSpringForce< DIM >::CalculateForceBetweenNodes().

template<unsigned DIM>

void MeshBasedTissue< DIM >::MarkSpring ( std::set< TissueCell * > & rCellPair ) [inline]

Mark the spring between the given cells.

Parameters:

rCellPair

a set of pointers to TissueCells

Definition at line 792 of file MeshBasedTissue.cpp.

References MeshBasedTissue< DIM >::mMarkedSprings.

Referenced by MeshBasedTissue< DIM >::AddCell().

template<unsigned DIM>

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

Remove all cells that are labelled as dead.

Note that this now calls MutableMesh::DeleteNodePriorToReMesh() and therefore a ReMesh(map) must be called before any element information is used.

Note also that after calling this method the tissue will be in an inconsistent state until Update() is called! So don't try iterating over cells or anything like that.

Returns:: number of cells removed.

Implements AbstractTissue< DIM >.

Definition at line 183 of file MeshBasedTissue.cpp.

References MutableMesh< ELEMENT_DIM, SPACE_DIM >::DeleteNodePriorToReMesh(), AbstractTissue< DIM >::mCellLocationMap, AbstractTissue< DIM >::mCells, AbstractTissue< DIM >::mLocationCellMap, MeshBasedTissue< DIM >::mMarkedSprings, and MeshBasedTissue< DIM >::mrMesh.

template<unsigned DIM>

const MutableMesh< DIM, DIM > & MeshBasedTissue< DIM >::rGetMesh ( ) const [inline]

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

Definition at line 177 of file MeshBasedTissue.cpp.

References MeshBasedTissue< DIM >::mrMesh.

template<unsigned DIM>

MutableMesh< DIM, DIM > & MeshBasedTissue< DIM >::rGetMesh ( ) [inline]

Returns:: reference to mrMesh.

Definition at line 171 of file MeshBasedTissue.cpp.

References MeshBasedTissue< DIM >::mrMesh.

Referenced by CryptStatistics::CellIsInSection(), CryptStatistics::CellIsInSectionPeriodic(), and CryptSimulation2d::WriteVisualizerSetupFile().

template<unsigned DIM>

VoronoiTessellation< DIM > & MeshBasedTissue< DIM >::rGetVoronoiTessellation ( ) [inline]

Returns:: mpVoronoiTessellation.

Definition at line 690 of file MeshBasedTissue.cpp.

References MeshBasedTissue< DIM >::mpVoronoiTessellation.

Referenced by MeshBasedTissue< DIM >::GetDampingConstant(), MeshBasedTissue< DIM >::WriteCellAreaResultsToFile(), MeshBasedTissue< DIM >::WriteTissueAreaResultsToFile(), and MeshBasedTissue< DIM >::WriteVoronoiResultsToFile().

template<unsigned DIM>

template<class Archive >

void MeshBasedTissue< 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 AbstractCellCentreBasedTissue< DIM >.

Reimplemented in MeshBasedTissueWithGhostNodes< DIM >, and MeshBasedTissueWithGhostNodes< 2 >.

Definition at line 70 of file MeshBasedTissue.hpp.

template<unsigned DIM>

void MeshBasedTissue< DIM >::SetAreaBasedDampingConstant ( bool useAreaBasedDampingConstant ) [inline]

Set method for mUseAreaBasedDampingConstant.

Parameters:

useAreaBasedDampingConstant

whether to use a viscosity that is linear in the cell area, rather than constant

Definition at line 81 of file MeshBasedTissue.cpp.

References MeshBasedTissue< DIM >::mUseAreaBasedDampingConstant.

template<unsigned DIM>

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

Overridden SetNode() method.

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

Parameters:

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

Implements AbstractTissue< DIM >.

Definition at line 96 of file MeshBasedTissue.cpp.

References MeshBasedTissue< DIM >::mrMesh, and MutableMesh< ELEMENT_DIM, SPACE_DIM >::SetNode().

template<unsigned DIM>

void MeshBasedTissue< DIM >::SetOutputTissueAreas ( bool writeTissueAreas )

Set method for mWriteTissueAreas.

Todo:: Extend this to 3D (possibly rename to SetOutputTissueVolumes?) - see also #738

Parameters:

writeTissueAreas

whether to output tissue area data

template<unsigned DIM>

void MeshBasedTissue< DIM >::SetOutputVoronoiData ( bool writeVoronoiData )

Set method for mWriteVoronoiData.

Parameters:

writeVoronoiData

whether to output cell area and perimeter information

template<unsigned DIM>

MeshBasedTissue< DIM >::SpringIterator MeshBasedTissue< DIM >::SpringsBegin ( ) [inline]

Returns:: iterator pointing to the first spring in the tissue

Definition at line 660 of file MeshBasedTissue.cpp.

References TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::EdgesBegin(), and MeshBasedTissue< DIM >::mrMesh.

Referenced by LinearSpringWithVariableSpringConstantsForce< DIM >::AddForceContribution(), and AbstractTwoBodyInteractionForce< DIM >::AddForceContribution().

template<unsigned DIM>

MeshBasedTissue< DIM >::SpringIterator MeshBasedTissue< DIM >::SpringsEnd ( ) [inline]

Returns:: iterator pointing to one past the last spring in the tissue

Definition at line 666 of file MeshBasedTissue.cpp.

References TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::EdgesEnd(), and MeshBasedTissue< DIM >::mrMesh.

Referenced by LinearSpringWithVariableSpringConstantsForce< DIM >::AddForceContribution(), and AbstractTwoBodyInteractionForce< DIM >::AddForceContribution().

template<unsigned DIM>

void MeshBasedTissue< DIM >::UnmarkSpring ( std::set< TissueCell * > & rCellPair ) [inline]

Stop marking the spring between the given cells.

Parameters:

rCellPair

a set of pointers to TissueCells

Definition at line 798 of file MeshBasedTissue.cpp.

References MeshBasedTissue< DIM >::mMarkedSprings.

Referenced by GeneralisedLinearSpringForce< DIM >::CalculateForceBetweenNodes().

template<unsigned DIM>

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

Overridden Update(bool hasHadBirthsOrDeaths) method. Fixes up the mappings between cells and nodes.

Parameters:

hasHadBirthsOrDeaths

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

Implements AbstractTissue< DIM >.

Definition at line 239 of file MeshBasedTissue.cpp.

References AbstractTissue< DIM >::Begin(), GenericEventHandler< 9, CellBasedEventHandler >::BeginEvent(), Node< SPACE_DIM >::ContainingElementsBegin(), Node< SPACE_DIM >::ContainingElementsEnd(), MeshBasedTissue< DIM >::CreateVoronoiTessellation(), AbstractTissue< DIM >::End(), GenericEventHandler< 9, CellBasedEventHandler >::EndEvent(), AbstractCellCentreBasedTissue< DIM >::GetNodeCorrespondingToCell(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNumAllNodes(), TissueConfig::Instance(), AbstractTissue< DIM >::mCellLocationMap, AbstractTissue< DIM >::mCells, AbstractTissue< DIM >::mLocationCellMap, MeshBasedTissue< DIM >::mMarkedSprings, MeshBasedTissue< DIM >::mrMesh, MeshBasedTissue< DIM >::mUseAreaBasedDampingConstant, MutableMesh< ELEMENT_DIM, SPACE_DIM >::ReMesh(), Node< SPACE_DIM >::rGetContainingElementIndices(), MeshBasedTissue< DIM >::UpdateGhostNodesAfterReMesh(), and MeshBasedTissue< DIM >::Validate().

template<unsigned DIM>

void MeshBasedTissue< DIM >::UpdateGhostNodesAfterReMesh ( NodeMap & rMap ) [inline, protected, virtual]

Update mIsGhostNode if required by a remesh.

Parameters:

rMap

A map between node indices before and after remesh

Reimplemented in MeshBasedTissueWithGhostNodes< DIM >, and MeshBasedTissueWithGhostNodes< 2 >.

Definition at line 349 of file MeshBasedTissue.cpp.

Referenced by MeshBasedTissue< DIM >::Update().

template<unsigned DIM>

bool MeshBasedTissue< DIM >::UseAreaBasedDampingConstant ( ) [inline]

Returns:: mUseAreaBasedDampingConstant.

Definition at line 75 of file MeshBasedTissue.cpp.

References MeshBasedTissue< DIM >::mUseAreaBasedDampingConstant.

template<unsigned DIM>

void MeshBasedTissue< DIM >::Validate ( ) [inline, protected, virtual]

Check consistency of our internal data structures. Each node must have a cell associated with it.

Implements AbstractTissue< DIM >.

Reimplemented in MeshBasedTissueWithGhostNodes< DIM >, and MeshBasedTissueWithGhostNodes< 2 >.

Definition at line 149 of file MeshBasedTissue.cpp.

References AbstractTissue< DIM >::Begin(), AbstractTissue< DIM >::End(), AbstractTissue< DIM >::GetLocationIndexUsingCell(), and MeshBasedTissue< DIM >::GetNumNodes().

Referenced by MeshBasedTissue< DIM >::MeshBasedTissue(), MeshBasedTissue< 2 >::serialize(), and MeshBasedTissue< DIM >::Update().

template<unsigned DIM>

void MeshBasedTissue< DIM >::WriteCellAreaResultsToFile ( ) [inline]

Write current results to mpCellAreasFile.

In 2D, the data is written in the form:

time cell0_id cell0_x cell0_y cell0_area cell1_id cell1_x cell1_y cell1_area ...

and similarly in 3D.

Definition at line 550 of file MeshBasedTissue.cpp.

References AbstractTissue< DIM >::Begin(), AbstractTissue< DIM >::End(), AbstractCellCentreBasedTissue< DIM >::GetLocationOfCellCentre(), SimulationTime::GetTime(), SimulationTime::Instance(), AbstractTissue< DIM >::mCellLocationMap, MeshBasedTissue< DIM >::mpCellAreasFile, and MeshBasedTissue< DIM >::rGetVoronoiTessellation().

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

template<unsigned DIM>

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

Overridden WriteResultsToFiles() method.

Todo:: implement writing of tissue/cell lengths in 1D (see also #738)

Todo:: implement writing of tissue/cell volumes in 3D (see also #738)

Reimplemented from AbstractTissue< DIM >.

Definition at line 416 of file MeshBasedTissue.cpp.

References AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetElementIteratorBegin(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetElementIteratorEnd(), MeshBasedTissue< DIM >::GetNode(), SimulationTime::GetTime(), TissueConfig::Instance(), SimulationTime::Instance(), AbstractTissue< DIM >::mLocationCellMap, MeshBasedTissue< DIM >::mpElementFile, MeshBasedTissue< DIM >::mpVoronoiTessellation, MeshBasedTissue< DIM >::mrMesh, MeshBasedTissue< DIM >::WriteCellAreaResultsToFile(), MeshBasedTissue< DIM >::WriteTissueAreaResultsToFile(), and MeshBasedTissue< DIM >::WriteVoronoiResultsToFile().

template<unsigned DIM>

void MeshBasedTissue< DIM >::WriteTissueAreaResultsToFile ( ) [inline]

Write current results to mpTissueAreasFile if in 2D.

The data is written in the form:

time total_area apoptotic_area

Definition at line 520 of file MeshBasedTissue.cpp.

References AbstractTissue< DIM >::Begin(), AbstractTissue< DIM >::End(), SimulationTime::GetTime(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetVolume(), SimulationTime::Instance(), AbstractTissue< DIM >::mCellLocationMap, MeshBasedTissue< DIM >::mpTissueAreasFile, MeshBasedTissue< DIM >::mrMesh, and MeshBasedTissue< DIM >::rGetVoronoiTessellation().

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

template<unsigned DIM>

void MeshBasedTissue< DIM >::WriteVoronoiResultsToFile ( ) [inline]

Write current results to mpVoronoiFile.

Definition at line 497 of file MeshBasedTissue.cpp.

References AbstractTissue< DIM >::Begin(), AbstractTissue< DIM >::End(), AbstractCellCentreBasedTissue< DIM >::GetLocationOfCellCentre(), SimulationTime::GetTime(), SimulationTime::Instance(), AbstractTissue< DIM >::mCellLocationMap, MeshBasedTissue< DIM >::mpVoronoiFile, and MeshBasedTissue< DIM >::rGetVoronoiTessellation().

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

Friends And Related Function Documentation

template<unsigned DIM>

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

Needed for serialization.

Reimplemented from AbstractCellCentreBasedTissue< DIM >.

Reimplemented in MeshBasedTissueWithGhostNodes< DIM >, and MeshBasedTissueWithGhostNodes< 2 >.

Definition at line 57 of file MeshBasedTissue.hpp.

Member Data Documentation

template<unsigned DIM>

bool MeshBasedTissue< DIM >::mDeleteMesh [protected]

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

Definition at line 105 of file MeshBasedTissue.hpp.

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

template<unsigned DIM>

std::set<std::set<TissueCell*> > MeshBasedTissue< DIM >::mMarkedSprings [protected]

Special springs that we want to keep track of for some reason. Currently used to track cells in the process of dividing (which are represented as two cells joined by a shorter spring).

Definition at line 112 of file MeshBasedTissue.hpp.

Referenced by MeshBasedTissue< DIM >::CheckTissueCellPointers(), MeshBasedTissue< DIM >::IsMarkedSpring(), MeshBasedTissue< DIM >::MarkSpring(), MeshBasedTissue< DIM >::RemoveDeadCells(), MeshBasedTissue< 2 >::serialize(), MeshBasedTissue< DIM >::UnmarkSpring(), and MeshBasedTissue< DIM >::Update().

template<unsigned DIM>

out_stream MeshBasedTissue< DIM >::mpCellAreasFile [protected]

Results file for cell area data.

Definition at line 124 of file MeshBasedTissue.hpp.

Referenced by MeshBasedTissue< DIM >::CloseOutputFiles(), MeshBasedTissue< DIM >::CreateOutputFiles(), and MeshBasedTissue< DIM >::WriteCellAreaResultsToFile().

template<unsigned DIM>

out_stream MeshBasedTissue< DIM >::mpElementFile [protected]

Results file for elements.

Definition at line 115 of file MeshBasedTissue.hpp.

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