#include <NodeBasedCellPopulation.hpp>

Inheritance diagram for NodeBasedCellPopulation< DIM >:

Collaboration diagram for NodeBasedCellPopulation< DIM >:

Public Member Functions
void	SetNode (unsigned nodeIndex, ChastePoint< DIM > &rNewLocation)
	NodeBasedCellPopulation (NodesOnlyMesh< DIM > &rMesh, std::vector< CellPtr > &rCells, const std::vector< unsigned > locationIndices=std::vector< unsigned >(), bool deleteMesh=false, bool validate=true)
	NodeBasedCellPopulation (NodesOnlyMesh< DIM > &rMesh)
virtual	~NodeBasedCellPopulation ()
NodesOnlyMesh< DIM > &	rGetMesh ()
const NodesOnlyMesh< DIM > &	rGetMesh () const
unsigned	GetNumNodes ()
Node< DIM > *	GetNode (unsigned index)
unsigned	RemoveDeadCells ()
void	Clear ()
void	Update (bool hasHadBirthsOrDeaths=true)
BoxCollection< DIM > *	GetBoxCollection ()
std::set< std::pair< Node< DIM > , Node< DIM > > > &	rGetNodePairs ()
void	OutputCellPopulationParameters (out_stream &rParamsFile)
double	GetMechanicsCutOffLength ()
void	SetMechanicsCutOffLength (double mechanicsCutOffLength)
bool	GetUseVariableRadii ()
void	SetUseVariableRadii (bool useVariableRadii=true)
double	GetWidth (const unsigned &rDimension)
std::set< unsigned >	GetNeighbouringNodeIndices (unsigned index)
virtual CellPtr	AddCell (CellPtr pNewCell, const c_vector< double, DIM > &rCellDivisionVector, CellPtr pParentCell)
double	GetVolumeOfCell (CellPtr pCell)
Protected Member Functions
virtual void	UpdateParticlesAfterReMesh (NodeMap &rMap)
virtual void	Validate ()
Private Member Functions
template<class Archive >
void	serialize (Archive &archive, const unsigned int version)
unsigned	AddNode (Node< DIM > *pNewNode)
void	SplitUpIntoBoxes (double cutOffLength, c_vector< double, 2 *DIM > domainSize)
void	FindMaxAndMin ()
void	WriteCellVolumeResultsToFile ()
void	WriteVtkResultsToFile ()
Private Attributes
NodesOnlyMesh< DIM > *	mpNodesOnlyMesh
c_vector< double, DIM >	mMinSpatialPositions
c_vector< double, DIM >	mMaxSpatialPositions
std::set< std::pair< Node< DIM > , Node< DIM > > >	mNodePairs
std::map< unsigned, std::set < unsigned > >	mNodeNeighbours
bool	mDeleteMesh
double	mMechanicsCutOffLength
bool	mUseVariableRadii
Friends
class	TestNodeBasedCellPopulation
class	TestBoxCollection
class	boost::serialization::access

Detailed Description

template<unsigned DIM>
class NodeBasedCellPopulation< DIM >

A NodeBasedCellPopulation is a CellPopulation consisting of only nodes in space with associated cells. There are no elements and no mesh.

Definition at line 51 of file NodeBasedCellPopulation.hpp.

Constructor & Destructor Documentation

template<unsigned DIM>

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

Default constructor.

Note that the cell population will take responsibility for freeing the memory used by the nodes.

Parameters:

rMesh	a mutable nodes-only mesh
rCells	a vector of cells
locationIndices	an optional vector of location indices that correspond to real cells
deleteMesh	whether to delete nodes-only mesh in destructor
validate	whether to call Validate() in the constructor or not

Definition at line 40 of file NodeBasedCellPopulation.cpp.

References NodeBasedCellPopulation< DIM >::mpNodesOnlyMesh, AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mrMesh, and NodeBasedCellPopulation< DIM >::Validate().

template<unsigned DIM>

NodeBasedCellPopulation< DIM >::NodeBasedCellPopulation ( NodesOnlyMesh< DIM > & rMesh )

Constructor for use by the de-serializer.

Parameters:

rMesh a mutable nodes-only mesh

Definition at line 58 of file NodeBasedCellPopulation.cpp.

References NodeBasedCellPopulation< DIM >::mpNodesOnlyMesh, and AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mrMesh.

template<unsigned DIM>

NodeBasedCellPopulation< DIM >::~NodeBasedCellPopulation ( ) [virtual]

Destructor.

Frees all our node memory.

Definition at line 69 of file NodeBasedCellPopulation.cpp.

Member Function Documentation

template<unsigned DIM>

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

Overridden AddCell() method.

Add a new cell to the cell population and update the vector of cell radii in the NodesOnlyMesh.

Parameters:

pNewCell	the cell to add
rCellDivisionVector	the position in space at which to put it
pParentCell	pointer to a parent cell - this is required for node-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 in NodeBasedCellPopulationWithParticles< DIM >.

Definition at line 664 of file NodeBasedCellPopulation.cpp.

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

template<unsigned DIM>

unsigned NodeBasedCellPopulation< DIM >::AddNode ( Node< DIM > * pNewNode ) [private]

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 285 of file NodeBasedCellPopulation.cpp.

template<unsigned DIM>

void NodeBasedCellPopulation< DIM >::Clear ( )

Reset the member variables mNodePairs and mpBoxCollection in the underlying mesh.

Definition at line 91 of file NodeBasedCellPopulation.cpp.

template<unsigned DIM>

void NodeBasedCellPopulation< DIM >::FindMaxAndMin ( ) [private]

Loops over nodes and sets mMinSpatialPositions and mMaxSpatialPositions

Definition at line 127 of file NodeBasedCellPopulation.cpp.

template<unsigned DIM>

BoxCollection< DIM > * NodeBasedCellPopulation< DIM >::GetBoxCollection ( )

Returns:: pointer to a node box collection.

Definition at line 302 of file NodeBasedCellPopulation.cpp.

template<unsigned DIM>

double NodeBasedCellPopulation< DIM >::GetMechanicsCutOffLength ( )

Returns:: mMechanicsCutOffLength

Definition at line 336 of file NodeBasedCellPopulation.cpp.

template<unsigned DIM>

std::set< unsigned > NodeBasedCellPopulation< DIM >::GetNeighbouringNodeIndices ( unsigned index ) [virtual]

Overridden GetNeighbouringNodeIndices() method.

Only returns nodes that are strictly touching each other.

Parameters:

index the node index

Returns:: the set of neighbouring node indices.

Implements AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >.

Definition at line 366 of file NodeBasedCellPopulation.cpp.

References EXCEPTION.

Referenced by BuskeCompressionForce< DIM >::AddForceContribution().

template<unsigned DIM>

Node< DIM > * NodeBasedCellPopulation< DIM >::GetNode ( unsigned index ) [virtual]

Overridden GetNode() method.

Parameters:

index global index of the specified node

Returns:: a pointer to the node with a given index.

Implements AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >.

Definition at line 165 of file NodeBasedCellPopulation.cpp.

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

template<unsigned DIM>

unsigned NodeBasedCellPopulation< DIM >::GetNumNodes ( ) [virtual]

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

Implements AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >.

Definition at line 291 of file NodeBasedCellPopulation.cpp.

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

template<unsigned DIM>

bool NodeBasedCellPopulation< DIM >::GetUseVariableRadii ( )

Returns:: mUseVariableRadii

Definition at line 342 of file NodeBasedCellPopulation.cpp.

template<unsigned DIM>

double NodeBasedCellPopulation< DIM >::GetVolumeOfCell ( CellPtr pCell ) [virtual]

Overridden GetVolumeOfCell() method.

Parameters:

pCell boost shared pointer to a cell

Implements AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >.

Definition at line 430 of file NodeBasedCellPopulation.cpp.

template<unsigned DIM>

double NodeBasedCellPopulation< DIM >::GetWidth ( const unsigned & rDimension ) [virtual]

Overridden GetWidth() method.

Calculate the 'width' of any dimension of the cell population by computing the maximum distance between any nodes in this dimension.

Parameters:

rDimension a dimension (0,1 or 2)

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

Implements AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >.

Definition at line 354 of file NodeBasedCellPopulation.cpp.

template<unsigned DIM>

void NodeBasedCellPopulation< DIM >::OutputCellPopulationParameters ( out_stream & rParamsFile ) [virtual]

Outputs CellPopulation parameters to file

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

Parameters:

rParamsFile the file stream to which the parameters are output

Reimplemented from AbstractCentreBasedCellPopulation< DIM >.

Reimplemented in NodeBasedCellPopulationWithBuskeUpdate< DIM >, and NodeBasedCellPopulationWithParticles< DIM >.

Definition at line 318 of file NodeBasedCellPopulation.cpp.

References AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::OutputCellPopulationParameters().

Referenced by NodeBasedCellPopulationWithParticles< DIM >::OutputCellPopulationParameters(), and NodeBasedCellPopulationWithBuskeUpdate< DIM >::OutputCellPopulationParameters().

template<unsigned DIM>

unsigned NodeBasedCellPopulation< DIM >::RemoveDeadCells ( ) [virtual]

Remove all cells labelled as dead.

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

Returns:: number of cells removed

Implements AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >.

Definition at line 258 of file NodeBasedCellPopulation.cpp.

template<unsigned DIM>

NodesOnlyMesh< DIM > & NodeBasedCellPopulation< DIM >::rGetMesh ( )

Returns:: reference to mrMesh.

Reimplemented from AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >.

Definition at line 79 of file NodeBasedCellPopulation.cpp.

template<unsigned DIM>

const NodesOnlyMesh< DIM > & NodeBasedCellPopulation< DIM >::rGetMesh ( ) const

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

Definition at line 85 of file NodeBasedCellPopulation.cpp.

template<unsigned DIM>

std::set< std::pair< Node< DIM > *, Node< DIM > * > > & NodeBasedCellPopulation< DIM >::rGetNodePairs ( ) [virtual]

Overridden rGetNodePairs method

Returns:: Node pairs for force calculation.

Implements AbstractCentreBasedCellPopulation< DIM >.

Definition at line 308 of file NodeBasedCellPopulation.cpp.

template<unsigned DIM>

template<class Archive >

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

Serialize the object and its member variables.

Note that serialization of the nodes is handled by load/save_construct_data, so we don't actually have to do anything here except delegate to the base class.

Parameters:

archive	the archive
version	the current version of this class

Reimplemented from AbstractCentreBasedCellPopulation< DIM >.

Reimplemented in NodeBasedCellPopulationWithBuskeUpdate< DIM >, and NodeBasedCellPopulationWithParticles< DIM >.

Definition at line 99 of file NodeBasedCellPopulation.hpp.

References NodeBasedCellPopulation< DIM >::mMechanicsCutOffLength, NodeBasedCellPopulation< DIM >::mUseVariableRadii, and NodeBasedCellPopulation< DIM >::Validate().

template<unsigned DIM>

void NodeBasedCellPopulation< DIM >::SetMechanicsCutOffLength ( double mechanicsCutOffLength )

Set mMechanicsCutOffLength.

Parameters:

mechanicsCutOffLength the new value of mMechanicsCutOffLength

Definition at line 329 of file NodeBasedCellPopulation.cpp.

template<unsigned DIM>

void NodeBasedCellPopulation< DIM >::SetNode	(	unsigned	nodeIndex,
		ChastePoint< DIM > &	rNewLocation
	)

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

Parameters:

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

Definition at line 171 of file NodeBasedCellPopulation.cpp.

template<unsigned DIM>

void NodeBasedCellPopulation< DIM >::SetUseVariableRadii ( bool useVariableRadii = true )

Set mUseVariableRadii.

Parameters:

useVariableRadii the new value of mUseVariableRadii

Definition at line 348 of file NodeBasedCellPopulation.cpp.

template<unsigned DIM>

void NodeBasedCellPopulation< DIM >::SplitUpIntoBoxes	(	double	cutOffLength,
		c_vector< double, 2 *DIM >	domainSize
	)		`[private]`

Method for Initially Splitting up cell population into neighbouring boxes, to decrease runtime.

Parameters:

cutOffLength	length of spring cut off between nodes
domainSize	c_vector of size 2*dimension reads minX, maxX, minY, maxY, etc

Definition at line 121 of file NodeBasedCellPopulation.cpp.

template<unsigned DIM>

void NodeBasedCellPopulation< DIM >::Update ( bool hasHadBirthsOrDeaths = true ) [virtual]

Remove nodes that have been marked as deleted and update the node cell map.

Parameters:

hasHadBirthsOrDeaths whether cell population has had Births Or Deaths

Todo:: we want to make mCellLocationMap private - we need to find a better way of doing this

Implements AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >.

Definition at line 177 of file NodeBasedCellPopulation.cpp.

References EXCEPTION.

template<unsigned DIM>

void NodeBasedCellPopulation< DIM >::UpdateParticlesAfterReMesh ( NodeMap & rMap ) [protected, virtual]

Update mIsParticle if required by a remesh.

Parameters:

rMap	A map between node indices before and after remesh

Reimplemented in NodeBasedCellPopulationWithParticles< DIM >.

Definition at line 297 of file NodeBasedCellPopulation.cpp.

template<unsigned DIM>

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

Check consistency of our internal data structures.

Implements AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >.

Reimplemented in NodeBasedCellPopulationWithParticles< DIM >.

Definition at line 97 of file NodeBasedCellPopulation.cpp.

References EXCEPTION.

Referenced by NodeBasedCellPopulation< DIM >::NodeBasedCellPopulation(), and NodeBasedCellPopulation< DIM >::serialize().

template<unsigned DIM>

void NodeBasedCellPopulation< DIM >::WriteCellVolumeResultsToFile ( ) [private, virtual]

Overridden WriteCellVolumeResultsToFile() method.

Implements AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >.

Definition at line 500 of file NodeBasedCellPopulation.cpp.

References SimulationTime::GetTime(), and SimulationTime::Instance().

template<unsigned DIM>

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

Overridden WriteVtkResultsToFile() method.

Implements AbstractCentreBasedCellPopulation< DIM >.

Reimplemented in NodeBasedCellPopulationWithParticles< DIM >.

Definition at line 537 of file NodeBasedCellPopulation.cpp.

References CellPropertyCollection::GetProperties(), CellPropertyCollection::GetProperty(), CellPropertyCollection::GetSize(), SimulationTime::GetTimeStepsElapsed(), SimulationTime::Instance(), and UNSIGNED_UNSET.

Friends And Related Function Documentation

template<unsigned DIM>

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

Needed for serialization.

Reimplemented from AbstractCentreBasedCellPopulation< DIM >.

Reimplemented in NodeBasedCellPopulationWithBuskeUpdate< DIM >, and NodeBasedCellPopulationWithParticles< DIM >.

Definition at line 88 of file NodeBasedCellPopulation.hpp.

Member Data Documentation

template<unsigned DIM>

bool NodeBasedCellPopulation< DIM >::mDeleteMesh [private]

Whether to delete the nodes-only mesh (taken in one of the constructors, defaults to false).

Definition at line 74 of file NodeBasedCellPopulation.hpp.

template<unsigned DIM>

c_vector<double, DIM> NodeBasedCellPopulation< DIM >::mMaxSpatialPositions [private]

Vector of maximal spatial positions in each dimension.

Definition at line 65 of file NodeBasedCellPopulation.hpp.

template<unsigned DIM>

double NodeBasedCellPopulation< DIM >::mMechanicsCutOffLength [private]

Mechanics cut off length. Used in order to calculate the BoxCollection.

Definition at line 80 of file NodeBasedCellPopulation.hpp.

Referenced by NodeBasedCellPopulation< DIM >::serialize().

template<unsigned DIM>

c_vector<double, DIM> NodeBasedCellPopulation< DIM >::mMinSpatialPositions [private]

Vector of minimal spatial positions in each dimension.

Definition at line 62 of file NodeBasedCellPopulation.hpp.

template<unsigned DIM>

std::map<unsigned, std::set<unsigned> > NodeBasedCellPopulation< DIM >::mNodeNeighbours [private]

Indices of neighbours of local nodes.

Definition at line 71 of file NodeBasedCellPopulation.hpp.

template<unsigned DIM>

std::set< std::pair<Node<DIM>*, Node<DIM>* > > NodeBasedCellPopulation< DIM >::mNodePairs [private]

Node pairs for force calculations.

Definition at line 68 of file NodeBasedCellPopulation.hpp.

template<unsigned DIM>

NodesOnlyMesh<DIM>* NodeBasedCellPopulation< DIM >::mpNodesOnlyMesh [private]

Static cast of the mesh from AbstractCellPopulation.

Definition at line 59 of file NodeBasedCellPopulation.hpp.

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

template<unsigned DIM>

bool NodeBasedCellPopulation< DIM >::mUseVariableRadii [private]

Whether or not to have cell radii updated from CellData defaults to false.

Definition at line 85 of file NodeBasedCellPopulation.hpp.

Referenced by NodeBasedCellPopulation< DIM >::serialize().

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

cell_based/src/population/NodeBasedCellPopulation.hpp
cell_based/src/population/NodeBasedCellPopulation.cpp

Public Member Functions

Protected Member Functions

Private Member Functions

Private Attributes

Friends

Detailed Description

template<unsigned DIM> class NodeBasedCellPopulation< DIM >

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation

template<unsigned DIM>
class NodeBasedCellPopulation< DIM >