NodeBasedCellPopulation< DIM > Class Template Reference

#include <NodeBasedCellPopulation.hpp>

Inherits AbstractCentreBasedCellPopulation< DIM >.

Inherited by NodeBasedCellPopulationWithBuskeUpdate< DIM >, and NodeBasedCellPopulationWithParticles< DIM >.

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

List of all members.

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 ()
virtual CellPtr GetCellUsingLocationIndex (unsigned index)
Node< DIM > * GetNode (unsigned index)
unsigned RemoveDeadCells ()
void Clear ()
void Update (bool hasHadBirthsOrDeaths=true)
std::vector< std::pair< Node
< DIM > *, Node< DIM > * > > & 		rGetNodePairs ()
void OutputCellPopulationParameters (out_stream &rParamsFile)
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 GetMechanicsCutOffLength ()
bool GetUseVariableRadii ()
void SetUseVariableRadii (bool useVariableRadii=true)
void SetLoadBalanceMesh (bool loadBalanceMesh)
void SetLoadBalanceFrequency (unsigned loadBalanceFrequency)
double GetWidth (const unsigned &rDimension)
c_vector< double, DIM > GetSizeOfCellPopulation ()
std::set< unsigned > GetNeighbouringNodeIndices (unsigned index)
virtual CellPtr AddCell (CellPtr pNewCell, const c_vector< double, DIM > &rCellDivisionVector, CellPtr pParentCell)
double GetVolumeOfCell (CellPtr pCell)
void SendCellsToNeighbourProcesses ()
void NonBlockingSendCellsToNeighbourProcesses ()
void GetReceivedCells ()
std::pair< CellPtr, Node< DIM > * > GetCellNodePair (unsigned nodeIndex)
void AddReceivedCells ()
virtual void UpdateCellProcessLocation ()

Protected Member Functions

virtual void UpdateParticlesAfterReMesh (NodeMap &rMap)
virtual void Validate ()

Protected Attributes

NodesOnlyMesh< DIM > * mpNodesOnlyMesh

Private Member Functions

template<class Archive >
void serialize (Archive &archive, const unsigned int version)
unsigned AddNode (Node< DIM > *pNewNode)
void AddMovedCell (CellPtr pCell, boost::shared_ptr< Node< DIM > > pNode)
void DeleteMovedCell (unsigned index)
void RefreshHaloCells ()
void AddNodeAndCellToSendRight (unsigned nodeIndex)
void AddNodeAndCellToSendLeft (unsigned nodeIndex)
void AddCellsToSendRight (std::vector< unsigned > &cellLocationIndices)
void AddCellsToSendLeft (std::vector< unsigned > &cellLocationIndices)
void AddReceivedHaloCells ()
void AddHaloCell (CellPtr pCell, boost::shared_ptr< Node< DIM > > pNode)
void UpdateMapsAfterRemesh (NodeMap &map)
virtual void WriteVtkResultsToFile (const std::string &rDirectory)

Private Attributes

c_vector< double, DIM > mMinSpatialPositions
c_vector< double, DIM > mMaxSpatialPositions
std::vector< std::pair< Node
< DIM > *, Node< DIM > * > > 		mNodePairs
std::map< unsigned, std::set
< unsigned > > 		mNodeNeighbours
bool mDeleteMesh
bool mUseVariableRadii
std::vector< std::pair
< CellPtr, Node< DIM > * > > 		mCellsToSendRight
std::vector< std::pair
< CellPtr, Node< DIM > * > > 		mCellsToSendLeft
boost::shared_ptr< std::vector
< std::pair< CellPtr, Node
< DIM > * > > > 		mpCellsRecvRight
boost::shared_ptr< std::vector
< std::pair< CellPtr, Node
< DIM > * > > > 		mpCellsRecvLeft
ObjectCommunicator
< std::vector< std::pair
< CellPtr, Node< DIM > * > > > 		mRightCommunicator
ObjectCommunicator
< std::vector< std::pair
< CellPtr, Node< DIM > * > > > 		mLeftCommunicator
std::vector< CellPtr > mHaloCells
std::map< unsigned, CellPtr > mLocationHaloCellMap
std::map< CellPtr, unsigned > mHaloCellLocationMap
bool mLoadBalanceMesh
unsigned mLoadBalanceFrequency

Static Private Attributes

static const unsigned mCellCommunicationTag = 123

Friends

class TestNodeBasedCellPopulation
class TestNodeBasedCellPopulationParallelMethods
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 56 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 
) [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
validate whether to call Validate() in the constructor or not

Definition at line 49 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  )  [inline]

Constructor for use by the de-serializer.

Parameters:
rMesh a mutable nodes-only mesh

Definition at line 69 of file NodeBasedCellPopulation.cpp.

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

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

Destructor.

Frees all our node memory.

Definition at line 80 of file NodeBasedCellPopulation.cpp.

References NodeBasedCellPopulation< DIM >::Clear(), NodeBasedCellPopulation< DIM >::mDeleteMesh, and AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mrMesh.

Member Function Documentation

template<unsigned DIM>
void NodeBasedCellPopulation< 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 307 of file NodeBasedCellPopulation.cpp.

template<unsigned DIM>
void NodeBasedCellPopulation< 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 301 of file NodeBasedCellPopulation.cpp.

template<unsigned DIM>
void NodeBasedCellPopulation< 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 295 of file NodeBasedCellPopulation.cpp.

template<unsigned DIM>
CellPtr NodeBasedCellPopulation< 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 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 625 of file NodeBasedCellPopulation.cpp.

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

template<unsigned DIM>
void NodeBasedCellPopulation< DIM >::AddCellsToSendLeft ( std::vector< unsigned > &  cellLocationIndices  )  [inline, private]

Add a collection of cells to send left

Parameters:
cellLocationIndices the list of location indices of cells to send.

Definition at line 891 of file NodeBasedCellPopulation.cpp.

References NodeBasedCellPopulation< DIM >::AddNodeAndCellToSendLeft(), and NodeBasedCellPopulation< DIM >::mCellsToSendLeft.

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

template<unsigned DIM>
void NodeBasedCellPopulation< DIM >::AddCellsToSendRight ( std::vector< unsigned > &  cellLocationIndices  )  [inline, private]

Add a collection of cells to send right

Parameters:
cellLocationIndices the list of location indices of cells to send.

Definition at line 880 of file NodeBasedCellPopulation.cpp.

References NodeBasedCellPopulation< DIM >::AddNodeAndCellToSendRight(), and NodeBasedCellPopulation< DIM >::mCellsToSendRight.

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

template<unsigned DIM>
void NodeBasedCellPopulation< DIM >::AddHaloCell ( CellPtr  pCell,
boost::shared_ptr< Node< DIM > >  pNode 
) [inline, private]

Add a single halo cell with its node to the halo structures on this process.

Parameters:
pCell the cell to add.
pNode the node to add.

Definition at line 932 of file NodeBasedCellPopulation.cpp.

References NodesOnlyMesh< SPACE_DIM >::AddHaloNode(), NodeBasedCellPopulation< DIM >::mHaloCellLocationMap, NodeBasedCellPopulation< DIM >::mHaloCells, NodeBasedCellPopulation< DIM >::mLocationHaloCellMap, and NodeBasedCellPopulation< DIM >::mpNodesOnlyMesh.

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

template<unsigned DIM>
void NodeBasedCellPopulation< DIM >::AddMovedCell ( CellPtr  pCell,
boost::shared_ptr< Node< DIM > >  pNode 
) [inline, private]

Add a moved cell to this process along with its node.

Parameters:
pCell the pointer to the cell that is to be added.
pNode the pointer to the node that is to be added.

Definition at line 647 of file NodeBasedCellPopulation.cpp.

References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::AddCellUsingLocationIndex(), NodesOnlyMesh< SPACE_DIM >::AddMovedNode(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mCells, and NodeBasedCellPopulation< DIM >::mpNodesOnlyMesh.

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

template<unsigned DIM>
unsigned NodeBasedCellPopulation< DIM >::AddNode ( Node< DIM > *  pNewNode  )  [inline, 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 247 of file NodeBasedCellPopulation.cpp.

References NodesOnlyMesh< SPACE_DIM >::AddNode(), and NodeBasedCellPopulation< DIM >::mpNodesOnlyMesh.

template<unsigned DIM>
void NodeBasedCellPopulation< DIM >::AddNodeAndCellToSendLeft ( unsigned  nodeIndex  )  [inline, private]

Add the node and cell with index nodeIndex to the list of cells to send to the process left.

Parameters:
nodeIndex the index of the node and cell to send.

Definition at line 788 of file NodeBasedCellPopulation.cpp.

References NodeBasedCellPopulation< DIM >::GetCellNodePair(), and NodeBasedCellPopulation< DIM >::mCellsToSendLeft.

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

template<unsigned DIM>
void NodeBasedCellPopulation< DIM >::AddNodeAndCellToSendRight ( unsigned  nodeIndex  )  [inline, private]

Add the node and cell with index nodeIndex to the list of cells to send to the process right.

Parameters:
nodeIndex the index of the node and cell to send.

Definition at line 780 of file NodeBasedCellPopulation.cpp.

References NodeBasedCellPopulation< DIM >::GetCellNodePair(), and NodeBasedCellPopulation< DIM >::mCellsToSendRight.

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

template<unsigned DIM>
void NodeBasedCellPopulation< DIM >::AddReceivedCells (  )  [inline]

Add the contents of mpCellsRecvRight and mpCellsRecvLeft to the local population.

Definition at line 796 of file NodeBasedCellPopulation.cpp.

References NodeBasedCellPopulation< DIM >::AddMovedCell(), PetscTools::AmMaster(), PetscTools::AmTopMost(), NodeBasedCellPopulation< DIM >::mpCellsRecvLeft, and NodeBasedCellPopulation< DIM >::mpCellsRecvRight.

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

template<unsigned DIM>
void NodeBasedCellPopulation< DIM >::AddReceivedHaloCells (  )  [inline, private]

Add halo cells to the halo structure on this process.

Definition at line 902 of file NodeBasedCellPopulation.cpp.

References NodeBasedCellPopulation< DIM >::AddHaloCell(), NodesOnlyMesh< SPACE_DIM >::AddHaloNodesToBoxes(), PetscTools::AmMaster(), PetscTools::AmTopMost(), NodeBasedCellPopulation< DIM >::GetReceivedCells(), NodeBasedCellPopulation< DIM >::mpCellsRecvLeft, NodeBasedCellPopulation< DIM >::mpCellsRecvRight, and NodeBasedCellPopulation< DIM >::mpNodesOnlyMesh.

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

template<unsigned DIM>
void NodeBasedCellPopulation< DIM >::Clear (  )  [inline]

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

Definition at line 102 of file NodeBasedCellPopulation.cpp.

References NodeBasedCellPopulation< DIM >::mNodePairs.

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

template<unsigned DIM>
void NodeBasedCellPopulation< DIM >::DeleteMovedCell ( unsigned  index  )  [inline, private]

Delete a cell and its associated node that have moved off this process.

Parameters:
index the location of the cell to be deleted

Definition at line 660 of file NodeBasedCellPopulation.cpp.

References NodesOnlyMesh< SPACE_DIM >::DeleteMovedNode(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetLocationIndexUsingCell(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mCells, NodeBasedCellPopulation< DIM >::mpNodesOnlyMesh, and AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::RemoveCellUsingLocationIndex().

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

template<unsigned DIM>
std::pair< CellPtr, Node< DIM > * > NodeBasedCellPopulation< DIM >::GetCellNodePair ( unsigned  nodeIndex  )  [inline]

Helper method to find and pack up nodes and cells together

Parameters:
nodeIndex the global index of the node.
Returns:
the pair.

Definition at line 768 of file NodeBasedCellPopulation.cpp.

References NodeBasedCellPopulation< DIM >::GetCellUsingLocationIndex(), and NodeBasedCellPopulation< DIM >::GetNode().

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

template<unsigned DIM>
CellPtr NodeBasedCellPopulation< DIM >::GetCellUsingLocationIndex ( unsigned  index  )  [inline, virtual]

Overridden method from AbstractCellPopulation so that we can access halo cells through this method.

Parameters:
index the global index of the node assocaited with a cell
Returns:
the (set of) cells to which the node is attached.

Reimplemented from AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >.

Definition at line 259 of file NodeBasedCellPopulation.cpp.

References NodeBasedCellPopulation< DIM >::mLocationHaloCellMap.

Referenced by NodeBasedCellPopulation< DIM >::GetCellNodePair(), NodeBasedCellPopulation< DIM >::Validate(), NodeVelocityWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), HeterotypicBoundaryLengthWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), and NodeBasedCellPopulationWithParticles< DIM >::WriteVtkResultsToFile().

template<unsigned DIM>
double NodeBasedCellPopulation< DIM >::GetMechanicsCutOffLength (  )  [inline]
Returns:
the maximum interaction distance between cells, defined in NodesOnlyMesh.

Definition at line 313 of file NodeBasedCellPopulation.cpp.

References NodesOnlyMesh< SPACE_DIM >::GetMaximumInteractionDistance(), and NodeBasedCellPopulation< DIM >::mpNodesOnlyMesh.

template<unsigned DIM>
std::set< unsigned > NodeBasedCellPopulation< DIM >::GetNeighbouringNodeIndices ( unsigned  index  )  [inline, 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 363 of file NodeBasedCellPopulation.cpp.

References EXCEPTION, NodesOnlyMesh< SPACE_DIM >::GetMaximumInteractionDistance(), NodeBasedCellPopulation< DIM >::GetNode(), Node< SPACE_DIM >::GetRadius(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetVectorFromAtoB(), NodeBasedCellPopulation< DIM >::mNodeNeighbours, NodeBasedCellPopulation< DIM >::mpNodesOnlyMesh, and Node< SPACE_DIM >::rGetLocation().

Referenced by BuskeCompressionForce< DIM >::AddForceContribution(), NodeBasedCellPopulation< DIM >::GetVolumeOfCell(), NodeBasedCellPopulationWithBuskeUpdate< DIM >::UpdateNodeLocations(), and HeterotypicBoundaryLengthWriter< ELEMENT_DIM, SPACE_DIM >::Visit().

template<unsigned DIM>
Node< DIM > * NodeBasedCellPopulation< DIM >::GetNode ( unsigned  index  )  [inline, 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 126 of file NodeBasedCellPopulation.cpp.

References NodesOnlyMesh< SPACE_DIM >::GetNodeOrHaloNode(), and NodeBasedCellPopulation< DIM >::mpNodesOnlyMesh.

Referenced by NodeBasedCellPopulationWithParticles< DIM >::AddCell(), NodeBasedCellPopulation< DIM >::AddCell(), NodeBasedCellPopulation< DIM >::GetCellNodePair(), NodeBasedCellPopulation< DIM >::GetNeighbouringNodeIndices(), NodeBasedCellPopulation< DIM >::GetVolumeOfCell(), NodeBasedCellPopulationWithParticles< DIM >::IsParticle(), NodeBasedCellPopulation< DIM >::Update(), NodeBasedCellPopulationWithBuskeUpdate< DIM >::UpdateNodeLocations(), NodeBasedCellPopulationWithParticles< DIM >::UpdateParticlePositions(), NodeBasedCellPopulationWithParticles< DIM >::Validate(), and HeterotypicBoundaryLengthWriter< ELEMENT_DIM, SPACE_DIM >::Visit().

template<unsigned DIM>
unsigned NodeBasedCellPopulation< DIM >::GetNumNodes (  )  [inline, virtual]
Returns:
the number of nodes in the cell population.

Implements AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >.

Definition at line 253 of file NodeBasedCellPopulation.cpp.

References NodesOnlyMesh< SPACE_DIM >::GetNumNodes(), and NodeBasedCellPopulation< DIM >::mpNodesOnlyMesh.

Referenced by NodeBasedCellPopulationWithBuskeUpdate< DIM >::UpdateNodeLocations(), NodeBasedCellPopulationWithParticles< DIM >::UpdateParticlePositions(), NodeBasedCellPopulationWithParticles< DIM >::WriteVtkResultsToFile(), and NodeBasedCellPopulation< DIM >::WriteVtkResultsToFile().

template<unsigned DIM>
void NodeBasedCellPopulation< DIM >::GetReceivedCells (  )  [inline]

Obtain proper cell/node pair objects from a previous call to NonBlockingSendCellsToNeighbourProcesses();

Definition at line 751 of file NodeBasedCellPopulation.cpp.

References PetscTools::AmMaster(), PetscTools::AmTopMost(), EXCEPTION, ObjectCommunicator< CLASS >::GetRecvObject(), NodeBasedCellPopulation< DIM >::mLeftCommunicator, NodeBasedCellPopulation< DIM >::mpCellsRecvLeft, NodeBasedCellPopulation< DIM >::mpCellsRecvRight, and NodeBasedCellPopulation< DIM >::mRightCommunicator.

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

template<unsigned DIM>
c_vector< double, DIM > NodeBasedCellPopulation< DIM >::GetSizeOfCellPopulation (  )  [inline]

Overridden GetSizeOfCellPopulation to work in parallel.

Returns:
the size of the cell population.

Reimplemented from AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >.

Definition at line 349 of file NodeBasedCellPopulation.cpp.

References PetscTools::GetWorld().

template<unsigned DIM>
bool NodeBasedCellPopulation< DIM >::GetUseVariableRadii (  )  [inline]
Returns:
mUseVariableRadii

Definition at line 319 of file NodeBasedCellPopulation.cpp.

References NodeBasedCellPopulation< DIM >::mUseVariableRadii.

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

Overridden GetVolumeOfCell() method.

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

Implements AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >.

Definition at line 429 of file NodeBasedCellPopulation.cpp.

References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetLocationIndexUsingCell(), NodeBasedCellPopulation< DIM >::GetNeighbouringNodeIndices(), NodeBasedCellPopulation< DIM >::GetNode(), Node< SPACE_DIM >::GetRadius(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetVectorFromAtoB(), NodeBasedCellPopulation< DIM >::mpNodesOnlyMesh, and Node< SPACE_DIM >::rGetLocation().

template<unsigned DIM>
double NodeBasedCellPopulation< DIM >::GetWidth ( const unsigned &  rDimension  )  [inline, 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 343 of file NodeBasedCellPopulation.cpp.

References NodesOnlyMesh< SPACE_DIM >::GetWidth(), and NodeBasedCellPopulation< DIM >::mpNodesOnlyMesh.

template<unsigned DIM>
void NodeBasedCellPopulation< DIM >::NonBlockingSendCellsToNeighbourProcesses (  )  [inline]

Send the contents of mCellsToSendRight/Left to neighbouring processes using asynchronous communication. mpCellsRecvLeft/Right will not be updated until the equivalent GetReceivedCells() is called.

Definition at line 718 of file NodeBasedCellPopulation.cpp.

References PetscTools::AmMaster(), PetscTools::AmTopMost(), EXCEPTION, PetscTools::GetMyRank(), ObjectCommunicator< CLASS >::IRecvObject(), ObjectCommunicator< CLASS >::ISendObject(), NodeBasedCellPopulation< DIM >::mCellsToSendLeft, NodeBasedCellPopulation< DIM >::mCellsToSendRight, NodeBasedCellPopulation< DIM >::mLeftCommunicator, and NodeBasedCellPopulation< DIM >::mRightCommunicator.

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

template<unsigned DIM>
void NodeBasedCellPopulation< 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 AbstractCentreBasedCellPopulation< DIM >.

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

Definition at line 284 of file NodeBasedCellPopulation.cpp.

References NodesOnlyMesh< SPACE_DIM >::GetMaximumInteractionDistance(), NodeBasedCellPopulation< DIM >::mpNodesOnlyMesh, and NodeBasedCellPopulation< DIM >::mUseVariableRadii.

template<unsigned DIM>
void NodeBasedCellPopulation< DIM >::RefreshHaloCells (  )  [inline, private]

Send and receive halo nodes with neighbours and populate memory structures to store them

Definition at line 862 of file NodeBasedCellPopulation.cpp.

References NodeBasedCellPopulation< DIM >::AddCellsToSendLeft(), NodeBasedCellPopulation< DIM >::AddCellsToSendRight(), NodesOnlyMesh< SPACE_DIM >::ClearHaloNodes(), NodeBasedCellPopulation< DIM >::mHaloCellLocationMap, NodeBasedCellPopulation< DIM >::mHaloCells, NodeBasedCellPopulation< DIM >::mLocationHaloCellMap, NodeBasedCellPopulation< DIM >::mpNodesOnlyMesh, NodeBasedCellPopulation< DIM >::NonBlockingSendCellsToNeighbourProcesses(), NodesOnlyMesh< SPACE_DIM >::rGetHaloNodesToSendLeft(), and NodesOnlyMesh< SPACE_DIM >::rGetHaloNodesToSendRight().

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

template<unsigned DIM>
unsigned NodeBasedCellPopulation< 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

Implements AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >.

Definition at line 216 of file NodeBasedCellPopulation.cpp.

References MutableMesh< ELEMENT_DIM, SPACE_DIM >::DeleteNodePriorToReMesh(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetLocationIndexUsingCell(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mCells, NodeBasedCellPopulation< DIM >::mpNodesOnlyMesh, AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::RemoveCellUsingLocationIndex(), and NodesOnlyMesh< SPACE_DIM >::SolveNodeMapping().

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

Definition at line 96 of file NodeBasedCellPopulation.cpp.

References NodeBasedCellPopulation< DIM >::mpNodesOnlyMesh.

template<unsigned DIM>
NodesOnlyMesh< DIM > & NodeBasedCellPopulation< DIM >::rGetMesh (  )  [inline]
Returns:
reference to mrMesh.

Reimplemented from AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >.

Definition at line 90 of file NodeBasedCellPopulation.cpp.

References NodeBasedCellPopulation< DIM >::mpNodesOnlyMesh.

Referenced by NodeBasedCellPopulationWithBuskeUpdate< DIM >::UpdateNodeLocations(), NodeVelocityWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), HeterotypicBoundaryLengthWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), NodeBasedCellPopulationWithParticles< DIM >::WriteVtkResultsToFile(), and NodeBasedCellPopulation< DIM >::WriteVtkResultsToFile().

template<unsigned DIM>
std::vector< std::pair< Node< DIM > *, Node< DIM > * > > & NodeBasedCellPopulation< DIM >::rGetNodePairs (  )  [inline, virtual]

Overridden rGetNodePairs method

Returns:
Node pairs for force calculation.

Implements AbstractCentreBasedCellPopulation< DIM >.

Definition at line 278 of file NodeBasedCellPopulation.cpp.

References NodeBasedCellPopulation< DIM >::mNodePairs.

template<unsigned DIM>
void NodeBasedCellPopulation< DIM >::SendCellsToNeighbourProcesses (  )  [inline]

Send the contents of mCellsToSendRight/Left to neighbouring processes and receive from them into mpCellsRecvRight/Left.

Definition at line 697 of file NodeBasedCellPopulation.cpp.

References PetscTools::AmMaster(), PetscTools::AmTopMost(), EXCEPTION, PetscTools::GetMyRank(), NodeBasedCellPopulation< DIM >::mCellCommunicationTag, NodeBasedCellPopulation< DIM >::mCellsToSendLeft, NodeBasedCellPopulation< DIM >::mCellsToSendRight, NodeBasedCellPopulation< DIM >::mLeftCommunicator, NodeBasedCellPopulation< DIM >::mpCellsRecvLeft, NodeBasedCellPopulation< DIM >::mpCellsRecvRight, NodeBasedCellPopulation< DIM >::mRightCommunicator, and ObjectCommunicator< CLASS >::SendRecvObject().

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

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 135 of file NodeBasedCellPopulation.hpp.

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

template<unsigned DIM>
void NodeBasedCellPopulation< DIM >::SetLoadBalanceFrequency ( unsigned  loadBalanceFrequency  )  [inline]

Set the freqeuncy, in number of time steps, with which the underlying mesh should be load balanced.

Parameters:
loadBalanceFrequency the frequency for load balancing.

Definition at line 337 of file NodeBasedCellPopulation.cpp.

References NodeBasedCellPopulation< DIM >::mLoadBalanceFrequency.

template<unsigned DIM>
void NodeBasedCellPopulation< DIM >::SetLoadBalanceMesh ( bool  loadBalanceMesh  )  [inline]

Set whether to carry out the dynamic load balance algorithm on this mesh when it is updated

Parameters:
loadBalanceMesh whether to do dynamic load balancing.

Definition at line 331 of file NodeBasedCellPopulation.cpp.

References NodeBasedCellPopulation< DIM >::mLoadBalanceMesh.

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

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 132 of file NodeBasedCellPopulation.cpp.

References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNode(), and NodeBasedCellPopulation< DIM >::mpNodesOnlyMesh.

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

template<unsigned DIM>
void NodeBasedCellPopulation< DIM >::SetUseVariableRadii ( bool  useVariableRadii = true  )  [inline]

Set mUseVariableRadii.

Parameters:
useVariableRadii the new value of mUseVariableRadii

Definition at line 325 of file NodeBasedCellPopulation.cpp.

References NodeBasedCellPopulation< DIM >::mUseVariableRadii.

template<unsigned DIM>
void NodeBasedCellPopulation< DIM >::Update ( bool  hasHadBirthsOrDeaths = true  )  [inline, 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

Implements AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >.

Definition at line 138 of file NodeBasedCellPopulation.cpp.

References NodeBasedCellPopulation< DIM >::AddReceivedHaloCells(), PetscTools::Barrier(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::Begin(), NodesOnlyMesh< SPACE_DIM >::CalculateBoundaryNodePairs(), NodesOnlyMesh< SPACE_DIM >::CalculateInteriorNodePairs(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::End(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetLocationIndexUsingCell(), NodeBasedCellPopulation< DIM >::GetNode(), SimulationTime::Instance(), NodesOnlyMesh< SPACE_DIM >::LoadBalanceMesh(), NodeBasedCellPopulation< DIM >::mLoadBalanceFrequency, NodeBasedCellPopulation< DIM >::mLoadBalanceMesh, NodeBasedCellPopulation< DIM >::mNodeNeighbours, NodeBasedCellPopulation< DIM >::mNodePairs, NodeBasedCellPopulation< DIM >::mpNodesOnlyMesh, NodeBasedCellPopulation< DIM >::mUseVariableRadii, NodeBasedCellPopulation< DIM >::RefreshHaloCells(), NodesOnlyMesh< SPACE_DIM >::UpdateBoxCollection(), and NodeBasedCellPopulation< DIM >::UpdateCellProcessLocation().

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

template<unsigned DIM>
void NodeBasedCellPopulation< DIM >::UpdateCellProcessLocation (  )  [inline, virtual]

Update which process each cell is owned by.

Reimplemented from AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >.

Definition at line 822 of file NodeBasedCellPopulation.cpp.

References NodeBasedCellPopulation< DIM >::AddCellsToSendLeft(), NodeBasedCellPopulation< DIM >::AddCellsToSendRight(), NodeBasedCellPopulation< DIM >::AddReceivedCells(), NodesOnlyMesh< SPACE_DIM >::CalculateNodesOutsideLocalDomain(), NodeBasedCellPopulation< DIM >::DeleteMovedCell(), NodesOnlyMesh< SPACE_DIM >::GetMaximumNodeIndex(), NodeBasedCellPopulation< DIM >::mpNodesOnlyMesh, NodesOnlyMesh< SPACE_DIM >::ReMesh(), NodesOnlyMesh< SPACE_DIM >::ResizeBoxCollection(), NodesOnlyMesh< SPACE_DIM >::rGetNodesToSendLeft(), NodesOnlyMesh< SPACE_DIM >::rGetNodesToSendRight(), NodeBasedCellPopulation< DIM >::SendCellsToNeighbourProcesses(), and NodeBasedCellPopulation< DIM >::UpdateMapsAfterRemesh().

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

template<unsigned DIM>
void NodeBasedCellPopulation< DIM >::UpdateMapsAfterRemesh ( NodeMap &  map  )  [inline, private]

Update the map between nodes and cells after a call to remesh.

Parameters:
map The node map from ReMesh.

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

Definition at line 184 of file NodeBasedCellPopulation.cpp.

References NodeMap::GetNewIndex(), NodeMap::IsDeleted(), NodeMap::IsIdentityMap(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mCellLocationMap, AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mCells, AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mLocationCellMap, AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::SetCellUsingLocationIndex(), NodeBasedCellPopulation< DIM >::UpdateParticlesAfterReMesh(), and NodeBasedCellPopulation< DIM >::Validate().

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

template<unsigned DIM>
void NodeBasedCellPopulation< DIM >::UpdateParticlesAfterReMesh ( NodeMap &  rMap  )  [inline, 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 273 of file NodeBasedCellPopulation.cpp.

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

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

Check consistency of our internal data structures.

Implements AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >.

Reimplemented in NodeBasedCellPopulationWithParticles< DIM >.

Definition at line 108 of file NodeBasedCellPopulation.cpp.

References EXCEPTION, NodeBasedCellPopulation< DIM >::GetCellUsingLocationIndex(), SimulationTime::Instance(), and AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mrMesh.

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

template<unsigned DIM>
void NodeBasedCellPopulation< 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 AbstractCentreBasedCellPopulation< DIM >.

Reimplemented in NodeBasedCellPopulationWithParticles< DIM >.

Definition at line 519 of file NodeBasedCellPopulation.cpp.

References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::Begin(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::End(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetLocationIndexUsingCell(), NodesOnlyMesh< SPACE_DIM >::GetMaximumNodeIndex(), PetscTools::GetMyRank(), NodeBasedCellPopulation< DIM >::GetNumNodes(), SimulationTime::GetTimeStepsElapsed(), SimulationTime::Instance(), PetscTools::IsSequential(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mCellWriters, NodeBasedCellPopulation< DIM >::mpNodesOnlyMesh, AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mpVtkMetaFile, NodesOnlyMesh< SPACE_DIM >::ReMesh(), NodeBasedCellPopulation< DIM >::rGetMesh(), and NodesOnlyMesh< SPACE_DIM >::SolveNodeMapping().

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 124 of file NodeBasedCellPopulation.hpp.

Member Data Documentation

template<unsigned DIM>
const unsigned NodeBasedCellPopulation< DIM >::mCellCommunicationTag = 123 [static, private]

The tag used to send and recieve cell information

Definition at line 106 of file NodeBasedCellPopulation.hpp.

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

template<unsigned DIM>
std::vector<std::pair<CellPtr, Node<DIM>* > > NodeBasedCellPopulation< DIM >::mCellsToSendLeft [private]

The cells to send to the left process

Definition at line 91 of file NodeBasedCellPopulation.hpp.

Referenced by NodeBasedCellPopulation< DIM >::AddCellsToSendLeft(), NodeBasedCellPopulation< DIM >::AddNodeAndCellToSendLeft(), NodeBasedCellPopulation< DIM >::NonBlockingSendCellsToNeighbourProcesses(), and NodeBasedCellPopulation< DIM >::SendCellsToNeighbourProcesses().

template<unsigned DIM>
std::vector<std::pair<CellPtr, Node<DIM>* > > NodeBasedCellPopulation< DIM >::mCellsToSendRight [private]

The cells to send to the right process

Definition at line 88 of file NodeBasedCellPopulation.hpp.

Referenced by NodeBasedCellPopulation< DIM >::AddCellsToSendRight(), NodeBasedCellPopulation< DIM >::AddNodeAndCellToSendRight(), NodeBasedCellPopulation< DIM >::NonBlockingSendCellsToNeighbourProcesses(), and NodeBasedCellPopulation< DIM >::SendCellsToNeighbourProcesses().

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 82 of file NodeBasedCellPopulation.hpp.

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

template<unsigned DIM>
std::map<CellPtr, unsigned> NodeBasedCellPopulation< DIM >::mHaloCellLocationMap [private]

Map halo cells back to location indices

Definition at line 115 of file NodeBasedCellPopulation.hpp.

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

template<unsigned DIM>
std::vector<CellPtr> NodeBasedCellPopulation< DIM >::mHaloCells [private]

Pointers to halo cells

Definition at line 109 of file NodeBasedCellPopulation.hpp.

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

template<unsigned DIM>
ObjectCommunicator<std::vector<std::pair<CellPtr, Node<DIM>* > > > NodeBasedCellPopulation< DIM >::mLeftCommunicator [private]

A communicator to send cells to the left hand process

Definition at line 103 of file NodeBasedCellPopulation.hpp.

Referenced by NodeBasedCellPopulation< DIM >::GetReceivedCells(), NodeBasedCellPopulation< DIM >::NonBlockingSendCellsToNeighbourProcesses(), and NodeBasedCellPopulation< DIM >::SendCellsToNeighbourProcesses().

template<unsigned DIM>
unsigned NodeBasedCellPopulation< DIM >::mLoadBalanceFrequency [private]

The frequency at which the mesh is rebalanced

Definition at line 121 of file NodeBasedCellPopulation.hpp.

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

template<unsigned DIM>
bool NodeBasedCellPopulation< DIM >::mLoadBalanceMesh [private]

Whether to load balance the underlying mesh dynamically

Definition at line 118 of file NodeBasedCellPopulation.hpp.

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

template<unsigned DIM>
std::map<unsigned, CellPtr> NodeBasedCellPopulation< DIM >::mLocationHaloCellMap [private]

Map location indices back to halo cells

Definition at line 112 of file NodeBasedCellPopulation.hpp.

Referenced by NodeBasedCellPopulation< DIM >::AddHaloCell(), NodeBasedCellPopulation< DIM >::GetCellUsingLocationIndex(), and NodeBasedCellPopulation< DIM >::RefreshHaloCells().

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

Vector of maximal spatial positions in each dimension.

Definition at line 73 of file NodeBasedCellPopulation.hpp.

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

Vector of minimal spatial positions in each dimension.

Definition at line 70 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 79 of file NodeBasedCellPopulation.hpp.

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

template<unsigned DIM>
std::vector< std::pair<Node<DIM>*, Node<DIM>* > > NodeBasedCellPopulation< DIM >::mNodePairs [private]

Node pairs for force calculations.

Definition at line 76 of file NodeBasedCellPopulation.hpp.

Referenced by NodeBasedCellPopulation< DIM >::Clear(), NodeBasedCellPopulation< DIM >::rGetNodePairs(), and NodeBasedCellPopulation< DIM >::Update().

template<unsigned DIM>
boost::shared_ptr<std::vector<std::pair<CellPtr, Node<DIM>* > > > NodeBasedCellPopulation< DIM >::mpCellsRecvLeft [private]

A pointer to the cells received from the left process

Definition at line 97 of file NodeBasedCellPopulation.hpp.

Referenced by NodeBasedCellPopulation< DIM >::AddReceivedCells(), NodeBasedCellPopulation< DIM >::AddReceivedHaloCells(), NodeBasedCellPopulation< DIM >::GetReceivedCells(), and NodeBasedCellPopulation< DIM >::SendCellsToNeighbourProcesses().

template<unsigned DIM>
boost::shared_ptr<std::vector<std::pair<CellPtr, Node<DIM>* > > > NodeBasedCellPopulation< DIM >::mpCellsRecvRight [private]

A shared pointer to the cells received from the right process

Definition at line 94 of file NodeBasedCellPopulation.hpp.

Referenced by NodeBasedCellPopulation< DIM >::AddReceivedCells(), NodeBasedCellPopulation< DIM >::AddReceivedHaloCells(), NodeBasedCellPopulation< DIM >::GetReceivedCells(), and NodeBasedCellPopulation< DIM >::SendCellsToNeighbourProcesses().

template<unsigned DIM>
NodesOnlyMesh<DIM>* NodeBasedCellPopulation< DIM >::mpNodesOnlyMesh [protected]

Static cast of the mesh from AbstractCellPopulation.

Definition at line 65 of file NodeBasedCellPopulation.hpp.

Referenced by NodeBasedCellPopulation< DIM >::AddHaloCell(), NodeBasedCellPopulation< DIM >::AddMovedCell(), NodeBasedCellPopulation< DIM >::AddNode(), NodeBasedCellPopulation< DIM >::AddReceivedHaloCells(), NodeBasedCellPopulation< DIM >::DeleteMovedCell(), NodeBasedCellPopulation< DIM >::GetMechanicsCutOffLength(), NodeBasedCellPopulation< DIM >::GetNeighbouringNodeIndices(), NodeBasedCellPopulation< DIM >::GetNode(), NodeBasedCellPopulation< DIM >::GetNumNodes(), NodeBasedCellPopulation< DIM >::GetVolumeOfCell(), NodeBasedCellPopulation< DIM >::GetWidth(), NodeBasedCellPopulation< DIM >::NodeBasedCellPopulation(), NodeBasedCellPopulation< DIM >::OutputCellPopulationParameters(), NodeBasedCellPopulation< DIM >::RefreshHaloCells(), NodeBasedCellPopulation< DIM >::RemoveDeadCells(), NodeBasedCellPopulation< DIM >::rGetMesh(), NodeBasedCellPopulation< DIM >::SetNode(), NodeBasedCellPopulation< DIM >::Update(), NodeBasedCellPopulation< DIM >::UpdateCellProcessLocation(), NodeBasedCellPopulationWithParticles< DIM >::WriteVtkResultsToFile(), and NodeBasedCellPopulation< DIM >::WriteVtkResultsToFile().

template<unsigned DIM>
ObjectCommunicator<std::vector<std::pair<CellPtr, Node<DIM>* > > > NodeBasedCellPopulation< DIM >::mRightCommunicator [private]

A communicator to send cells to the right hand process

Definition at line 100 of file NodeBasedCellPopulation.hpp.

Referenced by NodeBasedCellPopulation< DIM >::GetReceivedCells(), NodeBasedCellPopulation< DIM >::NonBlockingSendCellsToNeighbourProcesses(), and NodeBasedCellPopulation< DIM >::SendCellsToNeighbourProcesses().

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 >::GetUseVariableRadii(), NodeBasedCellPopulation< DIM >::OutputCellPopulationParameters(), NodeBasedCellPopulation< DIM >::serialize(), NodeBasedCellPopulation< DIM >::SetUseVariableRadii(), and NodeBasedCellPopulation< DIM >::Update().

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