NodeBasedCellPopulationWithBuskeUpdate< DIM > Class Template Reference

#include <NodeBasedCellPopulationWithBuskeUpdate.hpp>

Inherits NodeBasedCellPopulation< DIM >.

Collaboration diagram for NodeBasedCellPopulationWithBuskeUpdate< DIM >:

[legend]

List of all members.

Public Member Functions
	NodeBasedCellPopulationWithBuskeUpdate (NodesOnlyMesh< DIM > &rMesh, std::vector< CellPtr > &rCells, const std::vector< unsigned > locationIndices=std::vector< unsigned >(), bool deleteMesh=false)
	NodeBasedCellPopulationWithBuskeUpdate (NodesOnlyMesh< DIM > &rMesh)
virtual void	UpdateNodeLocations (const std::vector< c_vector< double, DIM > > &rNodeForces, double dt)
void	OutputCellPopulationParameters (out_stream &rParamsFile)
Private Member Functions
template<class Archive >
void	serialize (Archive &archive, const unsigned int version)
Friends
class	TestNodeBasedCellPopulationWithBuskeUpdate
class	boost::serialization::access

---

Detailed Description

template<unsigned DIM>
class NodeBasedCellPopulationWithBuskeUpdate< DIM >

A NodeBasedCellPopulationWithBuskeUpdate is a CellPopulation consisting of only nodes in space with associated cells. There are no elements and no mesh. The cell positions are updated according to Buske et al (2011) (doi:10.1371/journal.pcbi.1001045).

Definition at line 43 of file NodeBasedCellPopulationWithBuskeUpdate.hpp.

---

Constructor & Destructor Documentation

template<unsigned DIM>

NodeBasedCellPopulationWithBuskeUpdate< DIM >::NodeBasedCellPopulationWithBuskeUpdate	(	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 34 of file NodeBasedCellPopulationWithBuskeUpdate.cpp.

template<unsigned DIM>

NodeBasedCellPopulationWithBuskeUpdate< DIM >::NodeBasedCellPopulationWithBuskeUpdate

(

NodesOnlyMesh< DIM > &

rMesh

)

[inline]

Constructor for use by the de-serializer.

Parameters:

rMesh

a mutable nodes-only mesh

Definition at line 43 of file NodeBasedCellPopulationWithBuskeUpdate.cpp.

---

Member Function Documentation

template<unsigned DIM>

void NodeBasedCellPopulationWithBuskeUpdate< 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 180 of file NodeBasedCellPopulationWithBuskeUpdate.cpp.

template<unsigned DIM>

template<class Archive >

void NodeBasedCellPopulationWithBuskeUpdate< 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 61 of file NodeBasedCellPopulationWithBuskeUpdate.hpp.

template<unsigned DIM>

void NodeBasedCellPopulationWithBuskeUpdate< DIM >::UpdateNodeLocations	(	const std::vector< c_vector< double, DIM > > &	rNodeForces,
		double	dt
	)			[inline, virtual]

Overridden UpdateNodeLocations() method. To use the update from Buske et al (2011) (doi:10.1371/journal.pcbi.1001045).

Parameters:

	rNodeForces	a vector containing the force on each node in the cell population
	dt	the time step

Reimplemented from AbstractCentreBasedCellPopulation< DIM >.

Definition at line 50 of file NodeBasedCellPopulationWithBuskeUpdate.cpp.

References PetscMatTools::AddToElement(), AbstractCellPopulation< DIM >::Begin(), PetscTools::CreateAndSetVec(), AbstractCellPopulation< DIM >::End(), PetscMatTools::Finalise(), NodesOnlyMesh< SPACE_DIM >::GetCellRadius(), AbstractCentreBasedCellPopulation< DIM >::GetDampingConstant(), NodeBasedCellPopulation< DIM >::GetNeighbouringNodeIndices(), NodeBasedCellPopulation< DIM >::GetNode(), AbstractCellPopulation< DIM >::mCellLocationMap, OdeLinearSystemSolver::rGetForceVector(), OdeLinearSystemSolver::rGetLhsMatrix(), NodeBasedCellPopulation< DIM >::rGetMesh(), PetscVecTools::SetElement(), OdeLinearSystemSolver::SetInitialConditionVector(), NodeBasedCellPopulation< DIM >::SetNode(), and OdeLinearSystemSolver::SolveOneTimeStep().

---

Friends And Related Function Documentation

template<unsigned DIM>

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

Needed for serialization.

Reimplemented from NodeBasedCellPopulation< DIM >.

Definition at line 50 of file NodeBasedCellPopulationWithBuskeUpdate.hpp.

---

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

• cell_based/src/population/NodeBasedCellPopulationWithBuskeUpdate.hpp
• cell_based/src/population/NodeBasedCellPopulationWithBuskeUpdate.cpp