NodeBasedCellPopulationWithParticles< DIM > Class Template Reference

#include <NodeBasedCellPopulationWithParticles.hpp>

Inherits NodeBasedCellPopulation< DIM >.

Collaboration diagram for NodeBasedCellPopulationWithParticles< DIM >:

Public Member Functions
	NodeBasedCellPopulationWithParticles (NodesOnlyMesh< DIM > &rMesh, std::vector< CellPtr > &rCells, const std::vector< unsigned > locationIndices=std::vector< unsigned >(), bool deleteMesh=false)
	NodeBasedCellPopulationWithParticles (NodesOnlyMesh< DIM > &rMesh)
void	UpdateParticlePositions (double dt)
void	UpdateParticlesAfterReMesh (NodeMap &rMap)
void	UpdateNodeLocations (double dt)
bool	IsParticle (unsigned index)
std::set< unsigned >	GetParticleIndices ()
CellPtr	AddCell (CellPtr pNewCell, const c_vector< double, DIM > &rCellDivisionVector, CellPtr pParentCell)
virtual void	WriteVtkResultsToFile (const std::string &rDirectory)
void	OutputCellPopulationParameters (out_stream &rParamsFile)
Protected Member Functions
void	Validate ()
Private Member Functions
void	SetParticles (const std::set< unsigned > &rParticleIndices)
template<class Archive >
void	serialize (Archive &archive, const unsigned int version)
Friends
class	TestNodeBasedCellPopulationWithParticles
class	boost::serialization::access

Detailed Description

template<unsigned DIM>
class NodeBasedCellPopulationWithParticles< DIM >

A NodeBasedCellPopulationWithParticles is a NodeBasedCellPopulation with cells interacting with particles, such as ECM or fluid particles.

Definition at line 50 of file NodeBasedCellPopulationWithParticles.hpp.

Constructor & Destructor Documentation

template<unsigned DIM>

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

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

Definition at line 46 of file NodeBasedCellPopulationWithParticles.cpp.

References EXCEPT_IF_NOT, AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNodeIteratorBegin(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNodeIteratorEnd(), PetscTools::IsSequential(), NodeBasedCellPopulationWithParticles< DIM >::SetParticles(), and NodeBasedCellPopulationWithParticles< DIM >::Validate().

template<unsigned DIM>

NodeBasedCellPopulationWithParticles< DIM >::NodeBasedCellPopulationWithParticles ( NodesOnlyMesh< DIM > & rMesh ) [inline]

Constructor for use by the de-serializer.

Parameters:

rMesh

a mutable nodes-only mesh

Definition at line 91 of file NodeBasedCellPopulationWithParticles.cpp.

Member Function Documentation

template<unsigned DIM>

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

Overridden AddCell() method.

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

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 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 NodeBasedCellPopulation< DIM >.

Definition at line 170 of file NodeBasedCellPopulationWithParticles.cpp.

References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetLocationIndexUsingCell(), and NodeBasedCellPopulation< DIM >::GetNode().

template<unsigned DIM>

std::set< unsigned > NodeBasedCellPopulationWithParticles< DIM >::GetParticleIndices ( ) [inline]

Returns:: the indices of those nodes that are particles.

Definition at line 103 of file NodeBasedCellPopulationWithParticles.cpp.

References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mrMesh.

template<unsigned DIM>

bool NodeBasedCellPopulationWithParticles< DIM >::IsParticle ( unsigned index ) [inline, virtual]

IsParticle() method.

Find if a given node is a particle

Parameters:

index

the global index of a specified node

Returns:: whether the node is a particle

Reimplemented from AbstractCentreBasedCellPopulation< DIM >.

Definition at line 97 of file NodeBasedCellPopulationWithParticles.cpp.

References NodeBasedCellPopulation< DIM >::GetNode().

Referenced by NodeBasedCellPopulationWithParticles< DIM >::Validate(), and NodeBasedCellPopulationWithParticles< DIM >::WriteVtkResultsToFile().

template<unsigned DIM>

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

Outputs CellPopulation parameters to file

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

Parameters:

rParamsFile

the file stream to which the parameters are output

Reimplemented from NodeBasedCellPopulation< DIM >.

Definition at line 357 of file NodeBasedCellPopulationWithParticles.cpp.

template<unsigned DIM>

template<class Archive >

void NodeBasedCellPopulationWithParticles< 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 NodeBasedCellPopulation< DIM >.

Definition at line 81 of file NodeBasedCellPopulationWithParticles.hpp.

template<unsigned DIM>

void NodeBasedCellPopulationWithParticles< DIM >::SetParticles ( const std::set< unsigned > & rParticleIndices ) [inline, private]

Set the particles by taking in a set of which nodes indices are particles.

Parameters:

rParticleIndices

set of node indices corresponding to particles

Definition at line 121 of file NodeBasedCellPopulationWithParticles.cpp.

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

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

template<unsigned DIM>

void NodeBasedCellPopulationWithParticles< DIM >::UpdateNodeLocations ( double dt ) [inline, virtual]

Overridden UpdateNodeLocation() method.

Update the location of each node in the cell population given a two vectors of forces on cells and particles and a time step over which to integrate the equations of motion.

Parameters:

dt

time step

Reimplemented from AbstractCentreBasedCellPopulation< DIM >.

Definition at line 223 of file NodeBasedCellPopulationWithParticles.cpp.

References NodeBasedCellPopulationWithParticles< DIM >::UpdateParticlePositions().

template<unsigned DIM>

void NodeBasedCellPopulationWithParticles< DIM >::UpdateParticlePositions ( double dt ) [inline]