Chaste  Release::2017.1
Classes | Public Member Functions | Protected Member Functions | Protected Attributes | Private Member Functions | Friends | List of all members
MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM > Class Template Reference

#include <MeshBasedCellPopulation.hpp>

+ Inheritance diagram for MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >:
+ Collaboration diagram for MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >:

Classes

class  SpringIterator
 

Public Member Functions

 MeshBasedCellPopulation (MutableMesh< ELEMENT_DIM, SPACE_DIM > &rMesh, std::vector< CellPtr > &rCells, const std::vector< unsigned > locationIndices=std::vector< unsigned >(), bool deleteMesh=false, bool validate=true)
 
 MeshBasedCellPopulation (MutableMesh< ELEMENT_DIM, SPACE_DIM > &rMesh)
 
virtual ~MeshBasedCellPopulation ()
 
MutableMesh< ELEMENT_DIM, SPACE_DIM > & rGetMesh ()
 
const MutableMesh< ELEMENT_DIM, SPACE_DIM > & rGetMesh () const
 
virtual TetrahedralMesh< ELEMENT_DIM, SPACE_DIM > * GetTetrahedralMeshForPdeModifier ()
 
bool UseAreaBasedDampingConstant ()
 
unsigned AddNode (Node< SPACE_DIM > *pNewNode)
 
void SetNode (unsigned nodeIndex, ChastePoint< SPACE_DIM > &rNewLocation)
 
double GetDampingConstant (unsigned nodeIndex)
 
void SetAreaBasedDampingConstant (bool useAreaBasedDampingConstant)
 
virtual void OpenWritersFiles (OutputFileHandler &rOutputFileHandler)
 
virtual unsigned RemoveDeadCells ()
 
virtual CellPtr AddCell (CellPtr pNewCell, CellPtr pParentCell)
 
virtual void WriteResultsToFiles (const std::string &rDirectory)
 
virtual void AcceptPopulationWriter (boost::shared_ptr< AbstractCellPopulationWriter< ELEMENT_DIM, SPACE_DIM > > pPopulationWriter)
 
virtual void AcceptPopulationCountWriter (boost::shared_ptr< AbstractCellPopulationCountWriter< ELEMENT_DIM, SPACE_DIM > > pPopulationCountWriter)
 
virtual void AcceptCellWriter (boost::shared_ptr< AbstractCellWriter< ELEMENT_DIM, SPACE_DIM > > pCellWriter, CellPtr pCell)
 
virtual void Update (bool hasHadBirthsOrDeaths=true)
 
void TessellateIfNeeded ()
 
void DivideLongSprings (double springDivisionThreshold)
 
Node< SPACE_DIM > * GetNode (unsigned index)
 
unsigned GetNumNodes ()
 
virtual void WriteVtkResultsToFile (const std::string &rDirectory)
 
double GetVolumeOfCell (CellPtr pCell)
 
void CreateVoronoiTessellation ()
 
VertexMesh< ELEMENT_DIM, SPACE_DIM > * GetVoronoiTessellation ()
 
double GetVolumeOfVoronoiElement (unsigned index)
 
double GetSurfaceAreaOfVoronoiElement (unsigned index)
 
double GetVoronoiEdgeLength (unsigned index1, unsigned index2)
 
double GetWidth (const unsigned &rDimension)
 
virtual void WriteDataToVisualizerSetupFile (out_stream &pVizSetupFile)
 
SpringIterator SpringsBegin ()
 
SpringIterator SpringsEnd ()
 
void CheckCellPointers ()
 
double GetAreaBasedDampingConstantParameter ()
 
void SetAreaBasedDampingConstantParameter (double areaBasedDampingConstantParameter)
 
std::vector< std::pair< Node< SPACE_DIM > *, Node< SPACE_DIM > * > > & rGetNodePairs ()
 
void OutputCellPopulationParameters (out_stream &rParamsFile)
 
void SetWriteVtkAsPoints (bool writeVtkAsPoints)
 
bool GetWriteVtkAsPoints ()
 
void SetOutputMeshInVtk (bool outputMeshInVtk)
 
bool GetOutputMeshInVtk ()
 
std::set< unsigned > GetNeighbouringNodeIndices (unsigned index)
 
void CalculateRestLengths ()
 
double GetRestLength (unsigned indexA, unsigned indexB)
 
void SetRestLength (unsigned indexA, unsigned indexB, double restLength)
 
template<>
void CreateVoronoiTessellation ()
 
template<>
void CreateVoronoiTessellation ()
 
template<>
void CreateVoronoiTessellation ()
 
template<>
void CreateVoronoiTessellation ()
 
template<>
void CreateVoronoiTessellation ()
 
- Public Member Functions inherited from AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >
 AbstractCentreBasedCellPopulation (AbstractMesh< ELEMENT_DIM, SPACE_DIM > &rMesh, std::vector< CellPtr > &rCells, const std::vector< unsigned > locationIndices=std::vector< unsigned >())
 
c_vector< double, SPACE_DIM > GetLocationOfCellCentre (CellPtr pCell)
 
Node< SPACE_DIM > * GetNodeCorrespondingToCell (CellPtr pCell)
 
virtual double GetCellDataItemAtPdeNode (unsigned pdeNodeIndex, std::string &rVariableName, bool dirichletBoundaryConditionApplies=false, double dirichletBoundaryValue=0.0)
 
std::pair< CellPtr, CellPtr > CreateCellPair (CellPtr pCell1, CellPtr pCell2)
 
bool IsMarkedSpring (const std::pair< CellPtr, CellPtr > &rCellPair)
 
void MarkSpring (std::pair< CellPtr, CellPtr > &rCellPair)
 
void UnmarkSpring (std::pair< CellPtr, CellPtr > &rCellPair)
 
bool IsCellAssociatedWithADeletedLocation (CellPtr pCell)
 
virtual std::set< unsigned > GetNeighbouringLocationIndices (CellPtr pCell)
 
virtual void CheckForStepSizeException (unsigned nodeIndex, c_vector< double, SPACE_DIM > &rDisplacement, double dt)
 
virtual bool IsGhostNode (unsigned index)
 
virtual bool IsParticle (unsigned index)
 
double GetMeinekeDivisionSeparation ()
 
void SetMeinekeDivisionSeparation (double divisionSeparation)
 
boost::shared_ptr< AbstractCentreBasedDivisionRule< ELEMENT_DIM, SPACE_DIM > > GetCentreBasedDivisionRule ()
 
void SetCentreBasedDivisionRule (boost::shared_ptr< AbstractCentreBasedDivisionRule< ELEMENT_DIM, SPACE_DIM > > pCentreBasedDivisionRule)
 
virtual double GetDefaultTimeStep ()
 
- Public Member Functions inherited from AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_DIM >
 AbstractOffLatticeCellPopulation (AbstractMesh< ELEMENT_DIM, SPACE_DIM > &rMesh, std::vector< CellPtr > &rCells, const std::vector< unsigned > locationIndices=std::vector< unsigned >())
 
virtual void UpdateNodeLocations (double dt)
 
void SetDampingConstantNormal (double dampingConstantNormal)
 
void SetDampingConstantMutant (double dampingConstantMutant)
 
void SetAbsoluteMovementThreshold (double absoluteMovementThreshold)
 
double GetAbsoluteMovementThreshold ()
 
double GetDampingConstantNormal ()
 
double GetDampingConstantMutant ()
 
- Public Member Functions inherited from AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >
 AbstractCellPopulation (AbstractMesh< ELEMENT_DIM, SPACE_DIM > &rMesh, std::vector< CellPtr > &rCells, const std::vector< unsigned > locationIndices=std::vector< unsigned >())
 
virtual ~AbstractCellPopulation ()
 
void InitialiseCells ()
 
void SetDataOnAllCells (const std::string &rDataName, double dataValue)
 
AbstractMesh< ELEMENT_DIM, SPACE_DIM > & rGetMesh ()
 
virtual bool IsPdeNodeAssociatedWithNonApoptoticCell (unsigned pdeNodeIndex)
 
std::list< CellPtr > & rGetCells ()
 
std::vector< unsigned > GetCellMutationStateCount ()
 
std::vector< unsigned > GetCellProliferativeTypeCount ()
 
std::vector< unsigned > GetCellCyclePhaseCount ()
 
unsigned GetNumRealCells ()
 
unsigned GetNumAllCells ()
 
void SetCellAncestorsToLocationIndices ()
 
std::set< unsigned > GetCellAncestors ()
 
virtual CellPtr GetCellUsingLocationIndex (unsigned index)
 
std::set< CellPtr > GetCellsUsingLocationIndex (unsigned index)
 
virtual bool IsCellAttachedToLocationIndex (unsigned index)
 
void SetCellUsingLocationIndex (unsigned index, CellPtr pCell)
 
virtual void AddCellUsingLocationIndex (unsigned index, CellPtr pCell)
 
virtual void RemoveCellUsingLocationIndex (unsigned index, CellPtr pCell)
 
void MoveCellInLocationMap (CellPtr pCell, unsigned old_index, unsigned new_index)
 
unsigned GetLocationIndexUsingCell (CellPtr pCell)
 
boost::shared_ptr< CellPropertyRegistry > GetCellPropertyRegistry ()
 
void SetDefaultCellMutationStateAndProliferativeTypeOrdering ()
 
c_vector< double, SPACE_DIM > GetCentroidOfCellPopulation ()
 
virtual void UpdateCellProcessLocation ()
 
void CloseWritersFiles ()
 
void OutputCellPopulationInfo (out_stream &rParamsFile)
 
virtual void SimulationSetupHook (AbstractCellBasedSimulation< ELEMENT_DIM, SPACE_DIM > *pSimulation)
 
bool GetOutputResultsForChasteVisualizer ()
 
template<template< unsigned, unsigned > class T>
void AddPopulationWriter ()
 
template<template< unsigned, unsigned > class T>
void AddCellWriter ()
 
template<template< unsigned, unsigned > class T>
void AddCellPopulationCountWriter ()
 
void AddPopulationWriter (boost::shared_ptr< AbstractCellPopulationWriter< ELEMENT_DIM, SPACE_DIM > > pPopulationWriter)
 
void AddCellWriter (boost::shared_ptr< AbstractCellWriter< ELEMENT_DIM, SPACE_DIM > > pCellWriter)
 
void AddCellPopulationCountWriter (boost::shared_ptr< AbstractCellPopulationCountWriter< ELEMENT_DIM, SPACE_DIM > > pCellPopulationCountWriter)
 
template<template< unsigned, unsigned > class T>
bool HasWriter () const
 
void SetOutputResultsForChasteVisualizer (bool outputResultsForChasteVisualizer)
 
c_vector< double, SPACE_DIM > GetSizeOfCellPopulation ()
 
virtual bool IsRoomToDivide (CellPtr pCell)
 
std::pair< unsigned, unsigned > CreateOrderedPair (unsigned index1, unsigned index2)
 
Iterator Begin ()
 
Iterator End ()
 
- Public Member Functions inherited from Identifiable
virtual ~Identifiable ()
 
std::string GetIdentifier () const
 

Protected Member Functions

virtual void UpdateGhostNodesAfterReMesh (NodeMap &rMap)
 
virtual void Validate ()
 
- Protected Member Functions inherited from AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >
 AbstractCentreBasedCellPopulation (AbstractMesh< ELEMENT_DIM, SPACE_DIM > &rMesh)
 
virtual void AcceptCellWritersAcrossPopulation ()
 
- Protected Member Functions inherited from AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_DIM >
 AbstractOffLatticeCellPopulation (AbstractMesh< ELEMENT_DIM, SPACE_DIM > &rMesh)
 
- Protected Member Functions inherited from AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >
 AbstractCellPopulation (AbstractMesh< ELEMENT_DIM, SPACE_DIM > &rMesh)
 

Protected Attributes

VertexMesh< ELEMENT_DIM, SPACE_DIM > * mpVoronoiTessellation
 
MutableMesh< ELEMENT_DIM, SPACE_DIM > * mpMutableMesh
 
bool mDeleteMesh
 
std::map< std::pair< unsigned, unsigned >, double > mSpringRestLengths
 
bool mUseAreaBasedDampingConstant
 
double mAreaBasedDampingConstantParameter
 
bool mWriteVtkAsPoints
 
bool mOutputMeshInVtk
 
bool mHasVariableRestLength
 
std::vector< std::pair< Node< SPACE_DIM > *, Node< SPACE_DIM > * > > mNodePairs
 
- Protected Attributes inherited from AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >
double mMeinekeDivisionSeparation
 
std::set< std::pair< CellPtr, CellPtr > > mMarkedSprings
 
boost::shared_ptr< AbstractCentreBasedDivisionRule< ELEMENT_DIM, SPACE_DIM > > mpCentreBasedDivisionRule
 
- Protected Attributes inherited from AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_DIM >
double mDampingConstantNormal
 
double mDampingConstantMutant
 
double mAbsoluteMovementThreshold
 
- Protected Attributes inherited from AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >
std::map< unsigned, std::set< CellPtr > > mLocationCellMap
 
std::map< Cell *, unsigned > mCellLocationMap
 
AbstractMesh< ELEMENT_DIM, SPACE_DIM > & mrMesh
 
std::list< CellPtr > mCells
 
c_vector< double, SPACE_DIM > mCentroid
 
out_stream mpVtkMetaFile
 
boost::shared_ptr< CellPropertyRegistry > mpCellPropertyRegistry
 
bool mOutputResultsForChasteVisualizer
 
std::vector< boost::shared_ptr< AbstractCellWriter< ELEMENT_DIM, SPACE_DIM > > > mCellWriters
 
std::vector< boost::shared_ptr< AbstractCellPopulationWriter< ELEMENT_DIM, SPACE_DIM > > > mCellPopulationWriters
 
std::vector< boost::shared_ptr< AbstractCellPopulationCountWriter< ELEMENT_DIM, SPACE_DIM > > > mCellPopulationCountWriters
 

Private Member Functions

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

Friends

class TestMeshBasedCellPopulation
 
class boost::serialization::access
 

Detailed Description

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>
class MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >

A facade class encapsulating a mesh-based 'cell population'.

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

Definition at line 57 of file MeshBasedCellPopulation.hpp.

Constructor & Destructor Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::MeshBasedCellPopulation ( MutableMesh< ELEMENT_DIM, SPACE_DIM > &  rMesh,
std::vector< CellPtr > &  rCells,
const std::vector< unsigned >  locationIndices = std::vector<unsigned>(),
bool  deleteMesh = false,
bool  validate = true 
)

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

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

Parameters
rMesha mutable tetrahedral mesh
rCellscells corresponding to the nodes of the mesh
locationIndicesan optional vector of location indices that correspond to real cells
deleteMeshset to true if you want the cell population to free the mesh memory on destruction
validatewhether to validate the cell population

Definition at line 50 of file MeshBasedCellPopulation.cpp.

References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mCells, MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mpMutableMesh, AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mrMesh, MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::rGetMesh(), and MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::Validate().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::MeshBasedCellPopulation ( MutableMesh< ELEMENT_DIM, SPACE_DIM > &  rMesh)

Constructor for use by the de-serializer.

Parameters
rMesha mutable tetrahedral mesh.

Definition at line 83 of file MeshBasedCellPopulation.cpp.

References MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mDeleteMesh, MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mpMutableMesh, MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mpVoronoiTessellation, and AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mrMesh.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::~MeshBasedCellPopulation ( )
virtual

Destructor.

Definition at line 92 of file MeshBasedCellPopulation.cpp.

References MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mDeleteMesh, MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mpVoronoiTessellation, and AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mrMesh.

Member Function Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::AcceptCellWriter ( boost::shared_ptr< AbstractCellWriter< ELEMENT_DIM, SPACE_DIM > >  pCellWriter,
CellPtr  pCell 
)
virtual

A virtual method to accept a cell writer so it can write data from this object to file.

Parameters
pCellWriterthe population writer.
pCellthe cell whose data are being written.

Implements AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >.

Definition at line 586 of file MeshBasedCellPopulation.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::AcceptPopulationCountWriter ( boost::shared_ptr< AbstractCellPopulationCountWriter< ELEMENT_DIM, SPACE_DIM > >  pPopulationCountWriter)
virtual

A virtual method to accept a cell population count writer so it can write data from this object to file.

Parameters
pPopulationCountWriterthe population count writer.

Implements AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >.

Definition at line 580 of file MeshBasedCellPopulation.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::AcceptPopulationWriter ( boost::shared_ptr< AbstractCellPopulationWriter< ELEMENT_DIM, SPACE_DIM > >  pPopulationWriter)
virtual

A virtual method to accept a cell population writer so it can write data from this object to file.

Parameters
pPopulationWriterthe population writer.

Implements AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >.

Definition at line 574 of file MeshBasedCellPopulation.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
CellPtr MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::AddCell ( CellPtr  pNewCell,
CellPtr  pParentCell 
)
virtual

Overridden AddCell() method.

Add a new cell to the cell population and update mIsGhostNode.

Parameters
pNewCellthe cell to add
pParentCellpointer to a parent cell - this is required for mesh-based cell populations
Returns
address of cell as it appears in the cell list (internal of this method uses a copy constructor along the way)

Reimplemented from AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >.

Reimplemented in MeshBasedCellPopulationWithGhostNodes< DIM >.

Definition at line 527 of file MeshBasedCellPopulation.cpp.

References AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::AddCell(), AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::CreateCellPair(), and AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::MarkSpring().

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
unsigned MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::AddNode ( Node< SPACE_DIM > *  pNewNode)
virtual

Overridden AddNode() method.

Add a new node to the cell population.

Parameters
pNewNodepointer to the new node
Returns
global index of new node in cell population

Implements AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_DIM >.

Definition at line 116 of file MeshBasedCellPopulation.cpp.

References MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mpMutableMesh.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::CalculateRestLengths ( )

Populate mSpringRestLengths by looping over all springs and calculating the current length

Definition at line 1223 of file MeshBasedCellPopulation.cpp.

References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::CreateOrderedPair(), Node< SPACE_DIM >::GetIndex(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mHasVariableRestLength, MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mSpringRestLengths, MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::rGetMesh(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::SpringsBegin(), and MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::SpringsEnd().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::CheckCellPointers ( )

Helper method for use in debugging.

Definition at line 1070 of file MeshBasedCellPopulation.cpp.

References AbstractCellCycleModel::GetCell(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetCellUsingLocationIndex(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetLocationIndexUsingCell(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mCells, AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mMarkedSprings, and UNUSED_OPT.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>
void MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::CreateVoronoiTessellation ( )

Create a Voronoi tessellation of the mesh.

Referenced by MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetVolumeOfCell(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::TessellateIfNeeded(), VolumeTrackingModifier< DIM >::UpdateCellData(), and HeterotypicBoundaryLengthWriter< ELEMENT_DIM, SPACE_DIM >::Visit().

template<>
void MeshBasedCellPopulation< 2, 3 >::CreateVoronoiTessellation ( )

Can't tessellate 2d meshes in 3d space yet.

Definition at line 970 of file MeshBasedCellPopulation.cpp.

References NEVER_REACHED.

template<>
void MeshBasedCellPopulation< 3 >::CreateVoronoiTessellation ( )

The cylindrical mesh is only defined in 2D, hence there is a separate definition for this method in 3D, which doesn't have the capability of dealing with periodic boundaries in 3D. This is

Todo:
#1374.

Definition at line 983 of file MeshBasedCellPopulation.cpp.

References MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mpVoronoiTessellation, and AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mrMesh.

template<>
void MeshBasedCellPopulation< 1, 1 >::CreateVoronoiTessellation ( )

The VoronoiTessellation class is only defined in 2D or 3D, hence there are two definitions to this method (one templated and one not).

Definition at line 995 of file MeshBasedCellPopulation.cpp.

References NEVER_REACHED.

template<>
void MeshBasedCellPopulation< 1, 2 >::CreateVoronoiTessellation ( )

The VoronoiTessellation class is only defined in 2D or 3D, hence there are two definitions to this method (one templated and one not).

Definition at line 1009 of file MeshBasedCellPopulation.cpp.

References NEVER_REACHED.

template<>
void MeshBasedCellPopulation< 1, 3 >::CreateVoronoiTessellation ( )

The VoronoiTessellation class is only defined in 2D or 3D, hence there are two definitions to this method (one templated and one not).

Definition at line 1022 of file MeshBasedCellPopulation.cpp.

References NEVER_REACHED.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::DivideLongSprings ( double  springDivisionThreshold)

Divides springs longer than the given threshold

Parameters
springDivisionThresholda given threshold

Definition at line 444 of file MeshBasedCellPopulation.cpp.

References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::AddCellUsingLocationIndex(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::CreateOrderedPair(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetCellUsingLocationIndex(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mCells, MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mSpringRestLengths, CellPropertyCollection::RemoveProperty(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::rGetMesh(), and UNSIGNED_UNSET.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
double MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetAreaBasedDampingConstantParameter ( )
Returns
mAreaBasedDampingConstantParameter

Definition at line 1150 of file MeshBasedCellPopulation.cpp.

References MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mAreaBasedDampingConstantParameter.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
double MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetDampingConstant ( unsigned  nodeIndex)
virtual

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

Parameters
nodeIndexthe global index of this node
Returns
the damping constant for the given Cell.

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(3.0)/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 AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >.

Definition at line 128 of file MeshBasedCellPopulation.cpp.

References AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetDampingConstant(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetVolumeOfVoronoiElement(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mAreaBasedDampingConstantParameter, and MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mUseAreaBasedDampingConstant.

Referenced by NodeVelocityWriter< ELEMENT_DIM, SPACE_DIM >::Visit().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
std::set< unsigned > MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetNeighbouringNodeIndices ( unsigned  index)
virtual

Overridden GetNeighbouringNodeIndices() method.

Parameters
indexthe node index
Returns
the set of neighbouring node indices.

Implements AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >.

Definition at line 1194 of file MeshBasedCellPopulation.cpp.

References Node< SPACE_DIM >::ContainingElementsBegin(), Node< SPACE_DIM >::ContainingElementsEnd(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetElement(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNodeGlobalIndex(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), and AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mrMesh.

Referenced by DiscreteSystemForceCalculator::CalculateFtAndFn(), DiscreteSystemForceCalculator::GetSamplingAngles(), and HeterotypicBoundaryLengthWriter< ELEMENT_DIM, SPACE_DIM >::Visit().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
Node< SPACE_DIM > * MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetNode ( unsigned  index)
virtual

Overridden GetNode() method.

Parameters
indexglobal index of the specified Node
Returns
pointer to the Node with given index.

Implements AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >.

Definition at line 510 of file MeshBasedCellPopulation.cpp.

References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mrMesh.

Referenced by MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::Update(), CellPopulationElementWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), and VoronoiDataWriter< ELEMENT_DIM, SPACE_DIM >::Visit().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
unsigned MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetNumNodes ( )
virtual

Overridden GetNumNodes() method.

Returns
the number of nodes in the cell population.

Implements AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >.

Definition at line 516 of file MeshBasedCellPopulation.cpp.

References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mrMesh.

Referenced by DiscreteSystemForceCalculator::CalculateExtremalNormalForces(), CellwiseDataGradient< DIM >::SetupGradients(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::Validate(), and MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::WriteVtkResultsToFile().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
bool MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetOutputMeshInVtk ( )
Returns
mOutputMeshInVtk.

Definition at line 842 of file MeshBasedCellPopulation.cpp.

References MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mOutputMeshInVtk.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
double MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetRestLength ( unsigned  indexA,
unsigned  indexB 
)
Returns
the rest length for a given spring
Parameters
indexAindex of first node in pair
indexBindex of second node in pair

Definition at line 1251 of file MeshBasedCellPopulation.cpp.

References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::CreateOrderedPair(), EXCEPTION, MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mHasVariableRestLength, and MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mSpringRestLengths.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
double MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetSurfaceAreaOfVoronoiElement ( unsigned  index)
Returns
the surface area of the element of mpVoronoiTessellation associated with the node with this global index in the Delaunay mesh.

This method should be called instead of calling GetVoronoiTessellation()->GetSurfaceAreaOfElement() because the global indices of Delaunay nodes and Voronoi elements may not match, e.g. if a node is a ghost node or corresponds to a Voronoi face.

Parameters
indexa node global index

Definition at line 1045 of file MeshBasedCellPopulation.cpp.

References MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mpVoronoiTessellation.

Referenced by LinearSpringWithVariableSpringConstantsForce< DIM >::VariableSpringConstantMultiplicationFactor().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
TetrahedralMesh< ELEMENT_DIM, SPACE_DIM > * MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetTetrahedralMeshForPdeModifier ( )
virtual

Overridden GetTetrahedralMeshForPdeModifier() method.

Returns
a shared pointer to mpMutableMesh.

This method is called by AbstractGrowingDomainPdeModifier.

Implements AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >.

Reimplemented in MeshBasedCellPopulationWithGhostNodes< DIM >.

Definition at line 207 of file MeshBasedCellPopulation.cpp.

References MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mpMutableMesh.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
double MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetVolumeOfCell ( CellPtr  pCell)
virtual

Overridden GetVolumeOfCell() method.

Parameters
pCellboost shared pointer to a cell
Returns
volume via associated mesh element

Implements AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >.

Definition at line 760 of file MeshBasedCellPopulation.cpp.

References AbstractTetrahedralElement< ELEMENT_DIM, SPACE_DIM >::CalculateJacobian(), Node< SPACE_DIM >::ContainingElementsBegin(), Node< SPACE_DIM >::ContainingElementsEnd(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::CreateVoronoiTessellation(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetLocationIndexUsingCell(), AbstractTetrahedralElement< ELEMENT_DIM, SPACE_DIM >::GetVolume(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mpVoronoiTessellation, NEVER_REACHED, Node< SPACE_DIM >::rGetContainingElementIndices(), and MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::rGetMesh().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
double MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetVolumeOfVoronoiElement ( unsigned  index)
Returns
the volume (or area in 2D, or length in 1D) of the element of mpVoronoiTessellation associated with the node with this global index in the Delaunay mesh.

This method should be called instead of calling GetVoronoiTessellation()->GetVolumeOfElement() because the global indices of Delaunay nodes and Voronoi elements may not match, e.g. if a node is a ghost node or corresponds to a Voronoi face.

Todo:
This method is somewhat redundant following the introduction of the method GetVolumeOfCell() (see #1985).
Parameters
indexa node global index

Definition at line 1037 of file MeshBasedCellPopulation.cpp.

References MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mpVoronoiTessellation.

Referenced by MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetDampingConstant().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
double MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetVoronoiEdgeLength ( unsigned  index1,
unsigned  index2 
)
Returns
the length of the edge of mpVoronoiTessellation associated with the two nodes with these global indices in the Delaunay mesh.

This method should be called instead of calling GetVoronoiTessellation()->GetEdgeLength() because the global indices of Delaunay nodes and Voronoi elements may not match, e.g. if a node is a ghost node or corresponds to a Voronoi face.

Parameters
index1a node global index
index2a node global index

Definition at line 1053 of file MeshBasedCellPopulation.cpp.

References EXCEPTION, and MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mpVoronoiTessellation.

Referenced by LinearSpringWithVariableSpringConstantsForce< DIM >::VariableSpringConstantMultiplicationFactor(), and HeterotypicBoundaryLengthWriter< ELEMENT_DIM, SPACE_DIM >::Visit().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
VertexMesh< ELEMENT_DIM, SPACE_DIM > * MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetVoronoiTessellation ( )
Returns
a reference to mpVoronoiTessellation.

Definition at line 1030 of file MeshBasedCellPopulation.cpp.

References MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mpVoronoiTessellation.

Referenced by VoronoiDataWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), and CellPopulationAreaWriter< ELEMENT_DIM, SPACE_DIM >::Visit().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
double MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetWidth ( const unsigned &  rDimension)
virtual

Overridden GetWidth() method.

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

Parameters
rDimensiona dimension (0,1 or 2)
Returns
The maximum distance between any nodes in this dimension.

Implements AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >.

Definition at line 1186 of file MeshBasedCellPopulation.cpp.

References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mrMesh.

Referenced by MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::WriteDataToVisualizerSetupFile().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
bool MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetWriteVtkAsPoints ( )
Returns
mWriteVtkAsPoints.

Definition at line 830 of file MeshBasedCellPopulation.cpp.

References MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mWriteVtkAsPoints.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::OpenWritersFiles ( OutputFileHandler &  rOutputFileHandler)
virtual

Overridden OpenWritersFiles() method.

Open all files in mCellPopulationWriters and mCellWriters for writing (not appending).

Parameters
rOutputFileHandlerhandler for the directory in which to open this file.

Reimplemented from AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >.

Reimplemented in MeshBasedCellPopulationWithGhostNodes< DIM >.

Definition at line 549 of file MeshBasedCellPopulation.cpp.

References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mOutputResultsForChasteVisualizer, and AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::OpenWritersFiles().

Referenced by MeshBasedCellPopulationWithGhostNodes< DIM >::OpenWritersFiles().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::OutputCellPopulationParameters ( out_stream &  rParamsFile)
virtual

Outputs CellPopulation parameters to file

Parameters
rParamsFilethe file stream to which the parameters are output

Reimplemented from AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >.

Definition at line 1173 of file MeshBasedCellPopulation.cpp.

References MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mAreaBasedDampingConstantParameter, MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mHasVariableRestLength, MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mOutputMeshInVtk, MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mUseAreaBasedDampingConstant, MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mWriteVtkAsPoints, and AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::OutputCellPopulationParameters().

Referenced by MeshBasedCellPopulationWithGhostNodes< DIM >::OutputCellPopulationParameters().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
unsigned MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::RemoveDeadCells ( )
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 cell population 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 AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >.

Definition at line 213 of file MeshBasedCellPopulation.cpp.

References MutableMesh< ELEMENT_DIM, SPACE_DIM >::DeleteNodePriorToReMesh(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetLocationIndexUsingCell(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mCells, AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mMarkedSprings, AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mrMesh, and AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::RemoveCellUsingLocationIndex().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
MutableMesh< ELEMENT_DIM, SPACE_DIM > & MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::rGetMesh ( )
Returns
reference to mrMesh.

Definition at line 195 of file MeshBasedCellPopulation.cpp.

References MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mpMutableMesh.

Referenced by DiscreteSystemForceCalculator::CalculateFtAndFn(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::CalculateRestLengths(), CryptStatistics::CellIsInSection(), CryptStatistics::CellIsInSectionPeriodic(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::DivideLongSprings(), CryptStatistics::GetCryptSection(), DiscreteSystemForceCalculator::GetSamplingAngles(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetVolumeOfCell(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::MeshBasedCellPopulation(), CellwiseDataGradient< DIM >::SetupGradients(), CellPopulationElementWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), CellPopulationAreaWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), NodeVelocityWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), BoundaryNodeWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), NodeLocationWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), DiscreteSystemForceCalculator::WriteResultsToFile(), and MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::WriteVtkResultsToFile().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
const MutableMesh< ELEMENT_DIM, SPACE_DIM > & MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::rGetMesh ( ) const
Returns
const reference to mrMesh (used in archiving).

Definition at line 201 of file MeshBasedCellPopulation.cpp.

References MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mpMutableMesh.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
std::vector< std::pair< Node< SPACE_DIM > *, Node< SPACE_DIM > * > > & MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::rGetNodePairs ( )
virtual

Overridden rGetNodePairs method which uses the Delaunay triangulatiuon

Returns
Node pairs for force calculation.

Implements AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >.

Definition at line 1164 of file MeshBasedCellPopulation.cpp.

References MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mNodePairs, and NEVER_REACHED.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>
template<class Archive >
void MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::serialize ( Archive &  archive,
const unsigned int  version 
)
inlineprivate

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
archivethe archive
versionthe current version of this class

Definition at line 75 of file MeshBasedCellPopulation.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::SetAreaBasedDampingConstant ( bool  useAreaBasedDampingConstant)

Set method for mUseAreaBasedDampingConstant.

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

Definition at line 109 of file MeshBasedCellPopulation.cpp.

References MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mUseAreaBasedDampingConstant.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::SetAreaBasedDampingConstantParameter ( double  areaBasedDampingConstantParameter)

Set mAreaBasedDampingConstantParameter.

Parameters
areaBasedDampingConstantParameterthe new value of mAreaBasedDampingConstantParameter

Definition at line 1156 of file MeshBasedCellPopulation.cpp.

References MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mAreaBasedDampingConstantParameter.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::SetNode ( unsigned  nodeIndex,
ChastePoint< SPACE_DIM > &  rNewLocation 
)
virtual

Overridden SetNode() method.

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

Parameters
nodeIndexthe index of the node to be moved
rNewLocationthe new target location of the node

Implements AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_DIM >.

Definition at line 122 of file MeshBasedCellPopulation.cpp.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::SetOutputMeshInVtk ( bool  outputMeshInVtk)

Set mOutputMeshInVtk.

Parameters
outputMeshInVtkwhether to write cells as points in VTK

Definition at line 836 of file MeshBasedCellPopulation.cpp.

References MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mOutputMeshInVtk.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::SetRestLength ( unsigned  indexA,
unsigned  indexB,
double  restLength 
)

Helper method to modify the rest length of a given spring

Parameters
indexAindex of first node in pair
indexBindex of second node in pair
restLengththe new rest length

Definition at line 1275 of file MeshBasedCellPopulation.cpp.

References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::CreateOrderedPair(), EXCEPTION, EXPORT_TEMPLATE_CLASS_ALL_DIMS, MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mHasVariableRestLength, and MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mSpringRestLengths.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::SetWriteVtkAsPoints ( bool  writeVtkAsPoints)

Set mWriteVtkAsPoints.

Parameters
writeVtkAsPointswhether to write cells as points in VTK

Definition at line 824 of file MeshBasedCellPopulation.cpp.

References MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mWriteVtkAsPoints.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::SpringIterator MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::SpringsBegin ( )
Returns
iterator pointing to the first spring in the cell population

Definition at line 933 of file MeshBasedCellPopulation.cpp.

References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mrMesh, and MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::SpringIterator::SpringIterator().

Referenced by AbstractTwoBodyInteractionForce< ELEMENT_DIM, SPACE_DIM >::AddForceContribution(), LinearSpringWithVariableSpringConstantsForce< DIM >::AddForceContribution(), CryptProjectionForce::AddForceContribution(), and MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::CalculateRestLengths().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::SpringIterator MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::SpringsEnd ( )
Returns
iterator pointing to one past the last spring in the cell population

Definition at line 939 of file MeshBasedCellPopulation.cpp.

References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mrMesh, and MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::SpringIterator::SpringIterator().

Referenced by AbstractTwoBodyInteractionForce< ELEMENT_DIM, SPACE_DIM >::AddForceContribution(), LinearSpringWithVariableSpringConstantsForce< DIM >::AddForceContribution(), CryptProjectionForce::AddForceContribution(), and MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::CalculateRestLengths().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::TessellateIfNeeded ( )

Tessellates when required: if areas or volumes are needed for mUseAreaBasedDampingConstant; if a CellPopulationAreaWriter or CellVolumesWriter has been added to the population; or if Voronoi data are to be output.

Definition at line 427 of file MeshBasedCellPopulation.cpp.

References GenericEventHandler< 11, CellBasedEventHandler >::BeginEvent(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::CreateVoronoiTessellation(), GenericEventHandler< 11, CellBasedEventHandler >::EndEvent(), and MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mUseAreaBasedDampingConstant.

Referenced by MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::Update(), and MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::WriteResultsToFiles().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::Update ( bool  hasHadBirthsOrDeaths = true)
virtual

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

Parameters
hasHadBirthsOrDeaths- a bool saying whether cell population has had Births Or Deaths not needed in this cell population class
Todo:
check if there is a more efficient way of keeping track of node velocity information (#2404)

If node radii are set, then we must keep a record of these, since they will be cleared during the remeshing process. We then restore these attributes to the nodes after calling ReMesh().

At present, we check whether node radii are set by interrogating the radius of the first node in the mesh and asking if it is strictly greater than zero (the default value, as set in the NodeAttributes constructor). Hence, we assume that either ALL node radii are set, or NONE are.

Todo:
There may be a better way of checking if node radii are set (#2694)

Implements AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >.

Definition at line 272 of file MeshBasedCellPopulation.cpp.

References Node< SPACE_DIM >::ContainingElementsBegin(), Node< SPACE_DIM >::ContainingElementsEnd(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetNode(), AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetNodeCorrespondingToCell(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mCellLocationMap, AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mCells, AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mLocationCellMap, AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mMarkedSprings, AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mrMesh, MutableMesh< ELEMENT_DIM, SPACE_DIM >::ReMesh(), Node< SPACE_DIM >::rGetContainingElementIndices(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::SetCellUsingLocationIndex(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::SetMeshHasChangedSinceLoading(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::TessellateIfNeeded(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::UpdateGhostNodesAfterReMesh(), and MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::Validate().

Referenced by CellPopulationAdjacencyMatrixWriter< ELEMENT_DIM, SPACE_DIM >::Visit().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::UpdateGhostNodesAfterReMesh ( NodeMap &  rMap)
protectedvirtual

Update mIsGhostNode if required by a remesh.

Parameters
rMapA map between node indices before and after remesh

Reimplemented in MeshBasedCellPopulationWithGhostNodes< DIM >.

Definition at line 522 of file MeshBasedCellPopulation.cpp.

Referenced by MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::Update().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
bool MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::UseAreaBasedDampingConstant ( )
Returns
mUseAreaBasedDampingConstant.

Definition at line 103 of file MeshBasedCellPopulation.cpp.

References MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mUseAreaBasedDampingConstant.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::Validate ( )
protectedvirtual

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

Implements AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >.

Reimplemented in MeshBasedCellPopulationWithGhostNodes< DIM >.

Definition at line 175 of file MeshBasedCellPopulation.cpp.

References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::Begin(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::End(), EXCEPTION, AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetLocationIndexUsingCell(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), and SimulationTime::Instance().

Referenced by MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::MeshBasedCellPopulation(), MeshBasedCellPopulation< 2 >::serialize(), and MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::Update().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::WriteDataToVisualizerSetupFile ( out_stream &  pVizSetupFile)
virtual

Overridden WriteDataToVisualizerSetupFile() method. Write any data necessary to a visualization setup file. Used by AbstractCellBasedSimulation::WriteVisualizerSetupFile().

Parameters
pVizSetupFilea visualization setup file

Reimplemented from AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >.

Definition at line 848 of file MeshBasedCellPopulation.cpp.

References MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetWidth(), and AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mrMesh.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::WriteResultsToFiles ( const std::string &  rDirectory)
virtual

Overridden WriteResultsToFiles() method.

Parameters
rDirectorypathname of the output directory, relative to where Chaste output is stored

Reimplemented from AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >.

Definition at line 563 of file MeshBasedCellPopulation.cpp.

References SimulationTime::Instance(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mpVoronoiTessellation, MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::TessellateIfNeeded(), and AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::WriteResultsToFiles().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::WriteVtkResultsToFile ( const std::string &  rDirectory)
virtual

Overridden WriteVtkResultsToFile() method.

Parameters
rDirectorypathname of the output directory, relative to where Chaste output is stored

Implements AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >.

Reimplemented in MeshBasedCellPopulationWithGhostNodes< DIM >.

Definition at line 592 of file MeshBasedCellPopulation.cpp.

References VertexMeshWriter< ELEMENT_DIM, SPACE_DIM >::AddCellData(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::Begin(), NodesOnlyMesh< SPACE_DIM >::ConstructNodesWithoutMesh(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::End(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetCellUsingLocationIndex(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetLocationIndexUsingCell(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetNumAllCells(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), SimulationTime::GetTimeStepsElapsed(), SimulationTime::Instance(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mCellWriters, MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mOutputMeshInVtk, MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mpVoronoiTessellation, AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mpVtkMetaFile, AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mrMesh, MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mWriteVtkAsPoints, MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::rGetMesh(), VtkMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFilesUsingMesh(), and VertexMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteVtkUsingMesh().

Friends And Related Function Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>
friend class boost::serialization::access
friend

Needed for serialization.

Definition at line 62 of file MeshBasedCellPopulation.hpp.

Member Data Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>
double MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mAreaBasedDampingConstantParameter
protected

Non-dimensional parameter d0 for use in area-based damping constant calculations.

Definition at line 132 of file MeshBasedCellPopulation.hpp.

Referenced by MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetAreaBasedDampingConstantParameter(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetDampingConstant(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::OutputCellPopulationParameters(), MeshBasedCellPopulation< 2 >::serialize(), and MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::SetAreaBasedDampingConstantParameter().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>
bool MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mDeleteMesh
protected

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

Definition at line 121 of file MeshBasedCellPopulation.hpp.

Referenced by MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::MeshBasedCellPopulation(), and MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::~MeshBasedCellPopulation().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>
bool MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mHasVariableRestLength
protected

Whether springs have variable rest lengths.

Definition at line 141 of file MeshBasedCellPopulation.hpp.

Referenced by MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::CalculateRestLengths(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetRestLength(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::OutputCellPopulationParameters(), MeshBasedCellPopulation< 2 >::serialize(), and MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::SetRestLength().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>
std::vector< std::pair<Node<SPACE_DIM>*, Node<SPACE_DIM>* > > MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mNodePairs
protected

Node pairs for force calculations.

Definition at line 144 of file MeshBasedCellPopulation.hpp.

Referenced by MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::rGetNodePairs().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>
bool MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mOutputMeshInVtk
protected

Whether to output the underlying MutableMesh in VTK.

Definition at line 138 of file MeshBasedCellPopulation.hpp.

Referenced by MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetOutputMeshInVtk(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::OutputCellPopulationParameters(), MeshBasedCellPopulation< 2 >::serialize(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::SetOutputMeshInVtk(), and MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::WriteVtkResultsToFile().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>
MutableMesh<ELEMENT_DIM, SPACE_DIM>* MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mpMutableMesh
protected

Static cast of the mesh from AbstractCellPopulation

Definition at line 115 of file MeshBasedCellPopulation.hpp.

Referenced by MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::AddNode(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetTetrahedralMeshForPdeModifier(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::MeshBasedCellPopulation(), and MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::rGetMesh().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>
VertexMesh<ELEMENT_DIM, SPACE_DIM>* MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mpVoronoiTessellation
protected

Pointer to a VertexMesh object that stores the Voronoi tessellation that is dual to mrMesh. The tessellation is created by calling CreateVoronoiTessellation() and can be accessed by calling GetVoronoiTessellation().

The tessellation can be used to compute the area and perimeter (in 2D) or volume and surface area (in 3D) of the Voronoi element corresponding to each node in the Delaunay mesh (including ghost nodes) by calling the methods GetVolumeOfVoronoiElement() and GetSurfaceAreaOfVoronoiElement() respectively. Each of these methods should be called rather than the relevant method on the VertexMesh. This is because the index of a given Node in mrMesh may not equal the index of the corresponding VertexElement in mpVoronoiTessellation; a map between these indices may be accessed by calling the methods GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex() and GetVoronoiElementIndexCorrespondingToDelaunayNodeIndex() on mpVoronoiTessellation.

Definition at line 112 of file MeshBasedCellPopulation.hpp.

Referenced by MeshBasedCellPopulation< 2 >::CreateVoronoiTessellation(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::CreateVoronoiTessellation(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetSurfaceAreaOfVoronoiElement(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetVolumeOfCell(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetVolumeOfVoronoiElement(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetVoronoiEdgeLength(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetVoronoiTessellation(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::MeshBasedCellPopulation(), MeshBasedCellPopulation< 2 >::serialize(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::WriteResultsToFiles(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::WriteVtkResultsToFile(), and MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::~MeshBasedCellPopulation().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>
std::map<std::pair<unsigned,unsigned>, double> MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mSpringRestLengths
protected

Keeps track of the rest lengths of springs if these are being used in the simulation.

Definition at line 126 of file MeshBasedCellPopulation.hpp.

Referenced by MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::CalculateRestLengths(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::DivideLongSprings(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetRestLength(), MeshBasedCellPopulation< 2 >::serialize(), and MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::SetRestLength().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>
bool MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mUseAreaBasedDampingConstant
protected

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

Definition at line 129 of file MeshBasedCellPopulation.hpp.

Referenced by MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetDampingConstant(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::OutputCellPopulationParameters(), MeshBasedCellPopulation< 2 >::serialize(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::SetAreaBasedDampingConstant(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::TessellateIfNeeded(), and MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::UseAreaBasedDampingConstant().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>
bool MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mWriteVtkAsPoints
protected

Whether to write cells as points in VTK.

Definition at line 135 of file MeshBasedCellPopulation.hpp.

Referenced by MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetWriteVtkAsPoints(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::OutputCellPopulationParameters(), MeshBasedCellPopulation< 2 >::serialize(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::SetWriteVtkAsPoints(), and MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::WriteVtkResultsToFile().

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