VertexBasedCellPopulation< DIM > Class Template Reference

#include <VertexBasedCellPopulation.hpp>

Inherits AbstractOffLatticeCellPopulation< DIM >.

Collaboration diagram for VertexBasedCellPopulation< DIM >:
Collaboration graph
[legend]

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)
std::set< unsigned > GetNeighbouringLocationIndices (CellPtr pCell)
unsigned AddNode (Node< DIM > *pNewNode)
void UpdateNodeLocations (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)
virtual void OpenWritersFiles (OutputFileHandler &rOutputFileHandler)
virtual void AcceptPopulationWriter (boost::shared_ptr< AbstractCellPopulationWriter< DIM, DIM > > pPopulationWriter)
virtual void AcceptPopulationCountWriter (boost::shared_ptr< AbstractCellPopulationCountWriter< DIM, DIM > > pPopulationCountWriter)
virtual void AcceptCellWriter (boost::shared_ptr< AbstractCellWriter< DIM, DIM > > pCellWriter, CellPtr pCell)
double GetVolumeOfCell (CellPtr pCell)
std::vector< c_vector< double,
DIM > > 		GetLocationsOfT2Swaps ()
std::vector< unsigned > GetCellIdsOfT2Swaps ()
void AddLocationOfT2Swap (c_vector< double, DIM > locationOfT2Swap)
void AddCellIdOfT2Swap (unsigned idOfT2Swap)
void ClearLocationsAndCellIdsOfT2Swaps ()
bool GetOutputCellRearrangementLocations ()
void SetOutputCellRearrangementLocations (bool outputCellRearrangementLocations)
void OutputCellPopulationParameters (out_stream &rParamsFile)
double GetWidth (const unsigned &rDimension)
std::set< unsigned > GetNeighbouringNodeIndices (unsigned index)
TetrahedralMesh< DIM, DIM > * GetTetrahedralMeshUsingVertexMesh ()
boost::shared_ptr
< AbstractVertexBasedDivisionRule
< DIM > > 		GetVertexBasedDivisionRule ()
void SetVertexBasedDivisionRule (boost::shared_ptr< AbstractVertexBasedDivisionRule< DIM > > pVertexBasedDivisionRule)

Private Member Functions

virtual void WriteVtkResultsToFile (const std::string &rDirectory)
template<class Archive >
void serialize (Archive &archive, const unsigned int version)
void Validate ()

Private Attributes

bool mDeleteMesh
MutableVertexMesh< DIM, DIM > * mpMutableVertexMesh
bool mOutputCellRearrangementLocations
boost::shared_ptr
< AbstractVertexBasedDivisionRule
< DIM > > 		mpVertexBasedDivisionRule
std::vector< c_vector< double,
DIM > > 		mLocationsOfT2Swaps
std::vector< unsigned > mCellIdsOfT2Swaps

Friends

class TestVertexBasedDivisionRules
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 58 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

Definition at line 59 of file VertexBasedCellPopulation.cpp.

References AbstractCellPopulation< ELEMENT_DIM, ELEMENT_DIM >::AddCellUsingLocationIndex(), AbstractCellPopulation< ELEMENT_DIM, ELEMENT_DIM >::mCells, VertexBasedCellPopulation< DIM >::mpMutableVertexMesh, VertexBasedCellPopulation< DIM >::mpVertexBasedDivisionRule, AbstractCellPopulation< ELEMENT_DIM, ELEMENT_DIM >::mrMesh, and VertexBasedCellPopulation< DIM >::Validate().

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

Constructor for use by boost serialization ONLY!

Parameters:
rMesh a vertex mesh.

Definition at line 87 of file VertexBasedCellPopulation.cpp.

References VertexBasedCellPopulation< DIM >::mpMutableVertexMesh, and AbstractCellPopulation< ELEMENT_DIM, ELEMENT_DIM >::mrMesh.

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

Destructor, which frees any memory allocated by the constructor.

Definition at line 96 of file VertexBasedCellPopulation.cpp.

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

Member Function Documentation

template<unsigned DIM>
void VertexBasedCellPopulation< DIM >::AcceptCellWriter ( boost::shared_ptr< AbstractCellWriter< DIM, DIM > >  pCellWriter,
CellPtr  pCell 
) [inline, virtual]

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

Parameters:
pCellWriter the population writer.
pCell the cell whose data is being written.

Definition at line 386 of file VertexBasedCellPopulation.cpp.

template<unsigned DIM>
void VertexBasedCellPopulation< DIM >::AcceptPopulationCountWriter ( boost::shared_ptr< AbstractCellPopulationCountWriter< DIM, DIM > >  pPopulationCountWriter  )  [inline, virtual]

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

Parameters:
pPopulationCountWriter the population count writer.

Definition at line 380 of file VertexBasedCellPopulation.cpp.

template<unsigned DIM>
void VertexBasedCellPopulation< DIM >::AcceptPopulationWriter ( boost::shared_ptr< AbstractCellPopulationWriter< DIM, DIM > >  pPopulationWriter  )  [inline, virtual]

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

Parameters:
pPopulationWriter the population writer.

Definition at line 374 of file VertexBasedCellPopulation.cpp.

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

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)

Definition at line 208 of file VertexBasedCellPopulation.cpp.

References MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::DivideElementAlongGivenAxis(), VertexBasedCellPopulation< DIM >::GetElementCorrespondingToCell(), AbstractCellPopulation< ELEMENT_DIM, ELEMENT_DIM >::mCellLocationMap, AbstractCellPopulation< ELEMENT_DIM, ELEMENT_DIM >::mCells, VertexBasedCellPopulation< DIM >::mpMutableVertexMesh, and AbstractCellPopulation< ELEMENT_DIM, ELEMENT_DIM >::SetCellUsingLocationIndex().

template<unsigned DIM>
void VertexBasedCellPopulation< DIM >::AddCellIdOfT2Swap ( unsigned  idOfT2Swap  )  [inline]

Add ID of T2 Swap.

Parameters:
idOfT2Swap ID of the cell undergoing a T2 swap

Definition at line 591 of file VertexBasedCellPopulation.cpp.

References VertexBasedCellPopulation< DIM >::mCellIdsOfT2Swaps.

template<unsigned DIM>
void VertexBasedCellPopulation< DIM >::AddLocationOfT2Swap ( c_vector< double, DIM >  locationOfT2Swap  )  [inline]

Add location of T2 Swap.

Parameters:
locationOfT2Swap Location of the T2 swap

Definition at line 585 of file VertexBasedCellPopulation.cpp.

References VertexBasedCellPopulation< DIM >::mLocationsOfT2Swaps.

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

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

Definition at line 184 of file VertexBasedCellPopulation.cpp.

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

template<unsigned DIM>
void VertexBasedCellPopulation< DIM >::ClearLocationsAndCellIdsOfT2Swaps (  )  [inline]

Clear the locations and IDs of cells undergoing T2 Swaps.

Definition at line 597 of file VertexBasedCellPopulation.cpp.

References VertexBasedCellPopulation< DIM >::mCellIdsOfT2Swaps, and VertexBasedCellPopulation< DIM >::mLocationsOfT2Swaps.

Referenced by VertexT2SwapLocationsWriter< ELEMENT_DIM, SPACE_DIM >::Visit().

template<unsigned DIM>
std::vector< unsigned > VertexBasedCellPopulation< DIM >::GetCellIdsOfT2Swaps (  )  [inline]

Return all IDs of cells undergoing T2 Swaps since the last sampling time step.

Returns:
mLocationsOfT2Swaps

Definition at line 579 of file VertexBasedCellPopulation.cpp.

References VertexBasedCellPopulation< DIM >::mCellIdsOfT2Swaps.

Referenced by VertexT2SwapLocationsWriter< ELEMENT_DIM, SPACE_DIM >::Visit().

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 AbstractOffLatticeCellPopulation< DIM >.

Definition at line 105 of file VertexBasedCellPopulation.cpp.

References EXCEPTION, AbstractCellPopulation< ELEMENT_DIM, ELEMENT_DIM >::GetCellUsingLocationIndex(), AbstractOffLatticeCellPopulation< DIM >::GetDampingConstantMutant(), AbstractOffLatticeCellPopulation< DIM >::GetDampingConstantNormal(), VertexBasedCellPopulation< DIM >::GetNode(), and SimulationTime::Instance().

Referenced by VertexBasedCellPopulation< DIM >::UpdateNodeLocations(), and NodeVelocityWriter< ELEMENT_DIM, SPACE_DIM >::Visit().

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 153 of file VertexBasedCellPopulation.cpp.

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

Referenced by NagaiHondaForce< DIM >::AddForceContribution(), FarhadifarForce< DIM >::AddForceContribution(), VertexBasedCellPopulation< DIM >::RemoveDeadCells(), and CellPopulationElementWriter< ELEMENT_DIM, SPACE_DIM >::Visit().

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 196 of file VertexBasedCellPopulation.cpp.

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

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

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

Overridden GetLocationOfCellCentre() method.

Find the centre of mass of a given cell (assuming uniform density). Note that, as there is no guarantee of convexity, this may lie outside the VertexElement corresponding to the cell.

Parameters:
pCell a cell in the population
Returns:
the location of the centre of mass of the element corresponding to this cell.

Implements AbstractCellPopulation< ELEMENT_DIM, ELEMENT_DIM >.

Definition at line 165 of file VertexBasedCellPopulation.cpp.

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

template<unsigned DIM>
std::vector< c_vector< double, DIM > > VertexBasedCellPopulation< DIM >::GetLocationsOfT2Swaps (  )  [inline]

Return all locations of T2 Swaps since the last sampling time step.

Returns:
mLocationsOfT2Swaps

Definition at line 573 of file VertexBasedCellPopulation.cpp.

References VertexBasedCellPopulation< DIM >::mLocationsOfT2Swaps.

Referenced by VertexT2SwapLocationsWriter< ELEMENT_DIM, SPACE_DIM >::Visit().

template<unsigned DIM>
std::set< unsigned > VertexBasedCellPopulation< DIM >::GetNeighbouringLocationIndices ( CellPtr  pCell  )  [inline, virtual]

Overridden GetNeighbouringLocationIndices() method.

Given a cell, returns the set of location indices corresponding to neighbouring cells.

Parameters:
pCell a cell
Returns:
the set of neighbouring location indices.

Implements AbstractCellPopulation< ELEMENT_DIM, ELEMENT_DIM >.

Definition at line 177 of file VertexBasedCellPopulation.cpp.

References AbstractCellPopulation< ELEMENT_DIM, ELEMENT_DIM >::GetLocationIndexUsingCell(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetNeighbouringElementIndices(), and VertexBasedCellPopulation< DIM >::rGetMesh().

template<unsigned DIM>
std::set< unsigned > VertexBasedCellPopulation< DIM >::GetNeighbouringNodeIndices ( unsigned  index  )  [inline, virtual]

Overridden GetNeighbouringNodeIndices() method.

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

Implements AbstractCellPopulation< ELEMENT_DIM, ELEMENT_DIM >.

Definition at line 555 of file VertexBasedCellPopulation.cpp.

References VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetNeighbouringNodeIndices(), and VertexBasedCellPopulation< DIM >::mpMutableVertexMesh.

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< ELEMENT_DIM, ELEMENT_DIM >.

Definition at line 171 of file VertexBasedCellPopulation.cpp.

References AbstractCellPopulation< ELEMENT_DIM, ELEMENT_DIM >::mrMesh.

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

template<unsigned DIM>
unsigned VertexBasedCellPopulation< DIM >::GetNumElements (  )  [inline]
Returns:
the number of VertexElements in the cell population.

Definition at line 202 of file VertexBasedCellPopulation.cpp.

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

Referenced by NagaiHondaForce< DIM >::AddForceContribution(), FarhadifarForce< DIM >::AddForceContribution(), and 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< ELEMENT_DIM, ELEMENT_DIM >.

Definition at line 159 of file VertexBasedCellPopulation.cpp.

References AbstractCellPopulation< ELEMENT_DIM, ELEMENT_DIM >::mrMesh.

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

template<unsigned DIM>
bool VertexBasedCellPopulation< DIM >::GetOutputCellRearrangementLocations (  )  [inline]
Returns:
mOutputCellRearrangementLocations

Definition at line 517 of file VertexBasedCellPopulation.cpp.

References VertexBasedCellPopulation< DIM >::mOutputCellRearrangementLocations.

template<unsigned DIM>
TetrahedralMesh< DIM, DIM > * VertexBasedCellPopulation< DIM >::GetTetrahedralMeshUsingVertexMesh (  )  [inline]
Returns:
a tetrahedral mesh using the nodes in the VertexMesh as well as an additional node at the centre of each VertexElement. This method only works in 2D.

Todo:
will the nodes in mpMutableVertexMesh always have indices 0,1,2,...? (#2221)

Definition at line 604 of file VertexBasedCellPopulation.cpp.

References TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMeshReader(), AbstractCellPopulation< ELEMENT_DIM, ELEMENT_DIM >::CreateOrderedPair(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetCentroidOfElement(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetElement(), Node< SPACE_DIM >::GetIndex(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNode(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNodeGlobalIndex(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::GetNumElements(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), Node< SPACE_DIM >::IsBoundaryNode(), PetscTools::IsSequential(), VertexBasedCellPopulation< DIM >::mpMutableVertexMesh, Node< SPACE_DIM >::rGetLocation(), and AbstractMesh< ELEMENT_DIM, SPACE_DIM >::SetMeshHasChangedSinceLoading().

template<unsigned DIM>
boost::shared_ptr< AbstractVertexBasedDivisionRule< DIM > > VertexBasedCellPopulation< DIM >::GetVertexBasedDivisionRule (  )  [inline]
Returns:
The Vertex division rule that is currently being used.

Definition at line 561 of file VertexBasedCellPopulation.cpp.

References VertexBasedCellPopulation< DIM >::mpVertexBasedDivisionRule.

Referenced by OffLatticeSimulation< ELEMENT_DIM, SPACE_DIM >::CalculateCellDivisionVector().

template<unsigned DIM>
double VertexBasedCellPopulation< DIM >::GetVolumeOfCell ( CellPtr  pCell  )  [inline, virtual]

Overridden GetVolumeOfCell() method.

Parameters:
pCell boost shared pointer to a cell
Returns:
volume via associated mesh element

Implements AbstractCellPopulation< ELEMENT_DIM, ELEMENT_DIM >.

Definition at line 392 of file VertexBasedCellPopulation.cpp.

References AbstractCellPopulation< ELEMENT_DIM, ELEMENT_DIM >::GetLocationIndexUsingCell(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetVolumeOfElement(), and VertexBasedCellPopulation< DIM >::mpMutableVertexMesh.

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< ELEMENT_DIM, ELEMENT_DIM >.

Definition at line 546 of file VertexBasedCellPopulation.cpp.

References AbstractCellPopulation< ELEMENT_DIM, ELEMENT_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< ELEMENT_DIM, ELEMENT_DIM >.

Definition at line 306 of file VertexBasedCellPopulation.cpp.

References VertexBasedCellPopulation< DIM >::GetElementCorrespondingToCell().

template<unsigned DIM>
void VertexBasedCellPopulation< DIM >::OpenWritersFiles ( OutputFileHandler &  rOutputFileHandler  )  [inline, virtual]

Overridden OpenWritersFiles() method.

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

Parameters:
rOutputFileHandler handler for the directory in which to open this file.

Reimplemented from AbstractCellPopulation< ELEMENT_DIM, ELEMENT_DIM >.

Definition at line 487 of file VertexBasedCellPopulation.cpp.

References VertexBasedCellPopulation< DIM >::mOutputCellRearrangementLocations, and AbstractCellPopulation< ELEMENT_DIM, ELEMENT_DIM >::mOutputResultsForChasteVisualizer.

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

Overridden OutputCellPopulationParameters() method.

Parameters:
rParamsFile the file stream to which the parameters are output

Reimplemented from AbstractOffLatticeCellPopulation< DIM >.

Definition at line 529 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 >::mOutputCellRearrangementLocations, VertexBasedCellPopulation< DIM >::mpMutableVertexMesh, and VertexBasedCellPopulation< DIM >::mpVertexBasedDivisionRule.

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

Todo:
(#2489) this should cause an error - we should fix this!

Implements AbstractCellPopulation< ELEMENT_DIM, ELEMENT_DIM >.

Definition at line 230 of file VertexBasedCellPopulation.cpp.

References MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::DeleteElementPriorToReMesh(), VertexBasedCellPopulation< DIM >::GetElement(), AbstractCellPopulation< ELEMENT_DIM, ELEMENT_DIM >::GetLocationIndexUsingCell(), AbstractCellPopulation< ELEMENT_DIM, ELEMENT_DIM >::mCells, and VertexBasedCellPopulation< DIM >::mpMutableVertexMesh.

template<unsigned DIM>
const MutableVertexMesh< DIM, DIM > & VertexBasedCellPopulation< DIM >::rGetMesh (  )  const [inline]
Returns:
const reference to mrMesh (used in archiving).

Definition at line 147 of file VertexBasedCellPopulation.cpp.

References VertexBasedCellPopulation< DIM >::mpMutableVertexMesh.

template<unsigned DIM>
MutableVertexMesh< DIM, DIM > & VertexBasedCellPopulation< DIM >::rGetMesh (  )  [inline]
Returns:
reference to mrMesh.

Reimplemented from AbstractCellPopulation< ELEMENT_DIM, ELEMENT_DIM >.

Definition at line 141 of file VertexBasedCellPopulation.cpp.

References VertexBasedCellPopulation< DIM >::mpMutableVertexMesh.

Referenced by VertexCryptBoundaryForce< DIM >::AddForceContribution(), WelikyOsterForce< DIM >::AddForceContribution(), NagaiHondaForce< DIM >::AddForceContribution(), FarhadifarForce< DIM >::AddForceContribution(), ShortAxisVertexBasedDivisionRule< SPACE_DIM >::CalculateCellDivisionVector(), VertexBasedCellPopulation< DIM >::GetNeighbouringLocationIndices(), VertexT3SwapLocationsWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), VertexT1SwapLocationsWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), NodeVelocityWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), HeterotypicBoundaryLengthWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), and CellPopulationElementWriter< ELEMENT_DIM, SPACE_DIM >::Visit().

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 AbstractOffLatticeCellPopulation< DIM >.

Definition at line 118 of file VertexBasedCellPopulation.hpp.

References VertexBasedCellPopulation< DIM >::mOutputCellRearrangementLocations, and VertexBasedCellPopulation< DIM >::mpVertexBasedDivisionRule.

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

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

Definition at line 190 of file VertexBasedCellPopulation.cpp.

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

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

template<unsigned DIM>
void VertexBasedCellPopulation< DIM >::SetOutputCellRearrangementLocations ( bool  outputCellRearrangementLocations  )  [inline]

Set mOutputCellRearrangementLocations.

Parameters:
outputCellRearrangementLocations the new value of mOutputCellRearrangementLocations

Definition at line 523 of file VertexBasedCellPopulation.cpp.

References VertexBasedCellPopulation< DIM >::mOutputCellRearrangementLocations.

template<unsigned DIM>
void VertexBasedCellPopulation< DIM >::SetVertexBasedDivisionRule ( boost::shared_ptr< AbstractVertexBasedDivisionRule< DIM > >  pVertexBasedDivisionRule  )  [inline]

Set the division rule for this population.

Parameters:
pVertexBasedDivisionRule pointer to the new division rule

Definition at line 567 of file VertexBasedCellPopulation.cpp.

References VertexBasedCellPopulation< DIM >::mpVertexBasedDivisionRule.

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:
We want to make these maps private, so we need a better way of doing the code below.

Implements AbstractCellPopulation< ELEMENT_DIM, ELEMENT_DIM >.

Definition at line 312 of file VertexBasedCellPopulation.cpp.

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

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

template<unsigned DIM>
void VertexBasedCellPopulation< DIM >::UpdateNodeLocations ( double  dt  )  [inline, virtual]

Overridden UpdateNodeLocations() method.

Parameters:
dt the time step

Implements AbstractOffLatticeCellPopulation< DIM >.

Definition at line 265 of file VertexBasedCellPopulation.cpp.

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

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< ELEMENT_DIM, ELEMENT_DIM >.

Definition at line 346 of file VertexBasedCellPopulation.cpp.

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

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

template<unsigned DIM>
void VertexBasedCellPopulation< DIM >::WriteVtkResultsToFile ( const std::string &  rDirectory  )  [inline, private, virtual]

Overridden WriteVtkResultsToFile() method.

Parameters:
rDirectory pathname of the output directory, relative to where Chaste output is stored

Implements AbstractCellPopulation< ELEMENT_DIM, ELEMENT_DIM >.

Definition at line 404 of file VertexBasedCellPopulation.cpp.

References VertexMeshWriter< ELEMENT_DIM, SPACE_DIM >::AddCellData(), AbstractCellPopulation< ELEMENT_DIM, ELEMENT_DIM >::Begin(), AbstractCellPopulation< ELEMENT_DIM, ELEMENT_DIM >::GetCellUsingLocationIndex(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetElementIteratorBegin(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetElementIteratorEnd(), AbstractCellPopulation< ELEMENT_DIM, ELEMENT_DIM >::GetNumAllCells(), SimulationTime::GetTimeStepsElapsed(), SimulationTime::Instance(), AbstractCellPopulation< ELEMENT_DIM, ELEMENT_DIM >::mCellWriters, VertexBasedCellPopulation< DIM >::mpMutableVertexMesh, AbstractCellPopulation< ELEMENT_DIM, ELEMENT_DIM >::mpVtkMetaFile, and VertexMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteVtkUsingMesh().

Friends And Related Function Documentation

template<unsigned DIM>
friend class boost::serialization::access [friend]

Needed for serialization.

Reimplemented from AbstractOffLatticeCellPopulation< DIM >.

Definition at line 105 of file VertexBasedCellPopulation.hpp.

template<unsigned DIM>
friend class TestVertexBasedDivisionRules [friend]

This test uses the private constructor to simplify testing.

Definition at line 65 of file VertexBasedCellPopulation.hpp.

Member Data Documentation

template<unsigned DIM>
std::vector< unsigned > VertexBasedCellPopulation< DIM >::mCellIdsOfT2Swaps [private]

The Ids of cells that have undergone T2 swaps, stored so they can be accessed and output by the cell killer and population writer classes. The Ids are stored until they are cleared by ClearLocationsAndCellIdsOfT2Swaps().

Definition at line 96 of file VertexBasedCellPopulation.hpp.

Referenced by VertexBasedCellPopulation< DIM >::AddCellIdOfT2Swap(), VertexBasedCellPopulation< DIM >::ClearLocationsAndCellIdsOfT2Swaps(), and VertexBasedCellPopulation< DIM >::GetCellIdsOfT2Swaps().

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 71 of file VertexBasedCellPopulation.hpp.

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

template<unsigned DIM>
std::vector< c_vector<double, DIM> > VertexBasedCellPopulation< DIM >::mLocationsOfT2Swaps [private]

Locations of T2 swaps (the centre of the removed triangle), stored so they can be accessed and output by the cell killer and population writer classes. The locations are stored until they are cleared by ClearLocationsAndCellIdsOfT2Swaps().

Definition at line 90 of file VertexBasedCellPopulation.hpp.

Referenced by VertexBasedCellPopulation< DIM >::AddLocationOfT2Swap(), VertexBasedCellPopulation< DIM >::ClearLocationsAndCellIdsOfT2Swaps(), and VertexBasedCellPopulation< DIM >::GetLocationsOfT2Swaps().

template<unsigned DIM>
bool VertexBasedCellPopulation< DIM >::mOutputCellRearrangementLocations [private]

Whether to output the locations of T1 swaps and T3 swaps to files. Defaults to true.

Definition at line 80 of file VertexBasedCellPopulation.hpp.

Referenced by VertexBasedCellPopulation< DIM >::GetOutputCellRearrangementLocations(), VertexBasedCellPopulation< DIM >::OpenWritersFiles(), VertexBasedCellPopulation< DIM >::OutputCellPopulationParameters(), VertexBasedCellPopulation< DIM >::serialize(), and VertexBasedCellPopulation< DIM >::SetOutputCellRearrangementLocations().

template<unsigned DIM>
MutableVertexMesh<DIM, DIM>* VertexBasedCellPopulation< DIM >::mpMutableVertexMesh [private]

A static cast of the AbstractMesh from AbstractCellPopulation for use in this class

Definition at line 77 of file VertexBasedCellPopulation.hpp.

Referenced by VertexBasedCellPopulation< DIM >::AddCell(), VertexBasedCellPopulation< DIM >::AddNode(), VertexBasedCellPopulation< DIM >::GetElement(), VertexBasedCellPopulation< DIM >::GetElementCorrespondingToCell(), VertexBasedCellPopulation< DIM >::GetLocationOfCellCentre(), VertexBasedCellPopulation< DIM >::GetNeighbouringNodeIndices(), VertexBasedCellPopulation< DIM >::GetNumElements(), VertexBasedCellPopulation< DIM >::GetTetrahedralMeshUsingVertexMesh(), VertexBasedCellPopulation< DIM >::GetVolumeOfCell(), VertexBasedCellPopulation< DIM >::OutputCellPopulationParameters(), VertexBasedCellPopulation< DIM >::RemoveDeadCells(), VertexBasedCellPopulation< DIM >::rGetMesh(), VertexBasedCellPopulation< DIM >::SetNode(), VertexBasedCellPopulation< DIM >::Update(), VertexBasedCellPopulation< DIM >::UpdateNodeLocations(), VertexBasedCellPopulation< DIM >::VertexBasedCellPopulation(), and VertexBasedCellPopulation< DIM >::WriteVtkResultsToFile().

template<unsigned DIM>
boost::shared_ptr<AbstractVertexBasedDivisionRule<DIM> > VertexBasedCellPopulation< DIM >::mpVertexBasedDivisionRule [private]

A pointer to a division rule that is used to generate the axis when dividing cells. This is a specialisation for Vertex models.

Definition at line 84 of file VertexBasedCellPopulation.hpp.

Referenced by VertexBasedCellPopulation< DIM >::GetVertexBasedDivisionRule(), VertexBasedCellPopulation< DIM >::OutputCellPopulationParameters(), VertexBasedCellPopulation< DIM >::serialize(), VertexBasedCellPopulation< DIM >::SetVertexBasedDivisionRule(), and VertexBasedCellPopulation< DIM >::VertexBasedCellPopulation().

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