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Chaste Commit::333233612e3dcc941d260418acd7b5ccdc30390e
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#include <MeshBasedCellPopulation.hpp>
Classes | |
class | SpringIterator |
Public Member Functions | |
MeshBasedCellPopulation (MutableMesh< ELEMENT_DIM, SPACE_DIM > &rMesh, std::vector< CellPtr > &rCells, const std::vector< unsigned > locationIndices={}, bool deleteMesh=false, bool validate=true) | |
MeshBasedCellPopulation (MutableMesh< ELEMENT_DIM, SPACE_DIM > &rMesh) | |
virtual | ~MeshBasedCellPopulation () |
MutableMesh< ELEMENT_DIM, SPACE_DIM > & | rGetMesh () |
const MutableMesh< ELEMENT_DIM, SPACE_DIM > & | rGetMesh () const |
virtual TetrahedralMesh< ELEMENT_DIM, SPACE_DIM > * | GetTetrahedralMeshForPdeModifier () |
bool | UseAreaBasedDampingConstant () |
unsigned | AddNode (Node< SPACE_DIM > *pNewNode) |
void | SetNode (unsigned nodeIndex, ChastePoint< SPACE_DIM > &rNewLocation) |
double | GetDampingConstant (unsigned nodeIndex) |
void | SetAreaBasedDampingConstant (bool useAreaBasedDampingConstant) |
virtual void | OpenWritersFiles (OutputFileHandler &rOutputFileHandler) |
virtual unsigned | RemoveDeadCells () |
virtual CellPtr | AddCell (CellPtr pNewCell, CellPtr pParentCell) |
virtual void | WriteResultsToFiles (const std::string &rDirectory) |
virtual void | AcceptPopulationWriter (boost::shared_ptr< AbstractCellPopulationWriter< ELEMENT_DIM, SPACE_DIM > > pPopulationWriter) |
virtual void | AcceptPopulationCountWriter (boost::shared_ptr< AbstractCellPopulationCountWriter< ELEMENT_DIM, SPACE_DIM > > pPopulationCountWriter) |
virtual void | AcceptPopulationEventWriter (boost::shared_ptr< AbstractCellPopulationEventWriter< ELEMENT_DIM, SPACE_DIM > > pPopulationEventWriter) |
virtual void | AcceptCellWriter (boost::shared_ptr< AbstractCellWriter< ELEMENT_DIM, SPACE_DIM > > pCellWriter, CellPtr pCell) |
virtual void | Update (bool hasHadBirthsOrDeaths=true) |
void | TessellateIfNeeded () |
void | DivideLongSprings (double springDivisionThreshold) |
Node< SPACE_DIM > * | GetNode (unsigned index) |
unsigned | GetNumNodes () |
virtual void | WriteVtkResultsToFile (const std::string &rDirectory) |
double | GetVolumeOfCell (CellPtr pCell) |
void | CreateVoronoiTessellation () |
VertexMesh< ELEMENT_DIM, SPACE_DIM > * | GetVoronoiTessellation () |
double | GetVolumeOfVoronoiElement (unsigned index) |
double | GetSurfaceAreaOfVoronoiElement (unsigned index) |
double | GetVoronoiEdgeLength (unsigned index1, unsigned index2) |
double | GetWidth (const unsigned &rDimension) |
virtual void | WriteDataToVisualizerSetupFile (out_stream &pVizSetupFile) |
SpringIterator | SpringsBegin () |
SpringIterator | SpringsEnd () |
void | CheckCellPointers () |
double | GetAreaBasedDampingConstantParameter () |
void | SetAreaBasedDampingConstantParameter (double areaBasedDampingConstantParameter) |
std::vector< std::pair< Node< SPACE_DIM > *, Node< SPACE_DIM > * > > & | rGetNodePairs () |
void | OutputCellPopulationParameters (out_stream &rParamsFile) |
void | SetWriteVtkAsPoints (bool writeVtkAsPoints) |
bool | GetWriteVtkAsPoints () |
void | SetBoundVoronoiTessellation (bool boundVoronoiTessellation) |
bool | GetBoundVoronoiTessellation () |
void | SetScaleBoundByEdgeLength (bool scaleBoundByEdgeLength) |
bool | GetScaleBoundByEdgeLength () |
void | SetBoundedVoroniTesselationLengthCutoff (double boundedVoroniTesselationLengthCutoff) |
double | GetBoundedVoroniTesselationLengthCutoff () |
void | SetOffsetNewBoundaryNodes (bool offsetNewBoundaryNodes) |
bool | GetOffsetNewBoundaryNodes () |
std::set< unsigned > | GetNeighbouringNodeIndices (unsigned index) |
void | CalculateRestLengths () |
double | GetRestLength (unsigned indexA, unsigned indexB) |
void | SetRestLength (unsigned indexA, unsigned indexB, double restLength) |
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AbstractCentreBasedCellPopulation (AbstractMesh< ELEMENT_DIM, SPACE_DIM > &rMesh, std::vector< CellPtr > &rCells, const std::vector< unsigned > locationIndices=std::vector< unsigned >()) | |
c_vector< double, SPACE_DIM > | GetLocationOfCellCentre (CellPtr pCell) |
Node< SPACE_DIM > * | GetNodeCorrespondingToCell (CellPtr pCell) |
virtual double | GetCellDataItemAtPdeNode (unsigned pdeNodeIndex, std::string &rVariableName, bool dirichletBoundaryConditionApplies=false, double dirichletBoundaryValue=0.0) |
std::pair< CellPtr, CellPtr > | CreateCellPair (CellPtr pCell1, CellPtr pCell2) |
bool | IsMarkedSpring (const std::pair< CellPtr, CellPtr > &rCellPair) |
void | MarkSpring (std::pair< CellPtr, CellPtr > &rCellPair) |
void | UnmarkSpring (std::pair< CellPtr, CellPtr > &rCellPair) |
bool | IsCellAssociatedWithADeletedLocation (CellPtr pCell) |
virtual std::set< unsigned > | GetNeighbouringLocationIndices (CellPtr pCell) |
virtual void | CheckForStepSizeException (unsigned nodeIndex, c_vector< double, SPACE_DIM > &rDisplacement, double dt) |
virtual bool | IsGhostNode (unsigned index) |
virtual bool | IsParticle (unsigned index) |
double | GetMeinekeDivisionSeparation () |
void | SetMeinekeDivisionSeparation (double divisionSeparation) |
boost::shared_ptr< AbstractCentreBasedDivisionRule< ELEMENT_DIM, SPACE_DIM > > | GetCentreBasedDivisionRule () |
void | SetCentreBasedDivisionRule (boost::shared_ptr< AbstractCentreBasedDivisionRule< ELEMENT_DIM, SPACE_DIM > > pCentreBasedDivisionRule) |
virtual double | GetDefaultTimeStep () |
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AbstractOffLatticeCellPopulation (AbstractMesh< ELEMENT_DIM, SPACE_DIM > &rMesh, std::vector< CellPtr > &rCells, const std::vector< unsigned > locationIndices=std::vector< unsigned >()) | |
virtual void | UpdateNodeLocations (double dt) |
void | SetDampingConstantNormal (double dampingConstantNormal) |
void | SetDampingConstantMutant (double dampingConstantMutant) |
void | SetAbsoluteMovementThreshold (double absoluteMovementThreshold) |
double | GetAbsoluteMovementThreshold () |
double | GetDampingConstantNormal () |
double | GetDampingConstantMutant () |
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AbstractCellPopulation (AbstractMesh< ELEMENT_DIM, SPACE_DIM > &rMesh, std::vector< CellPtr > &rCells, const std::vector< unsigned > locationIndices=std::vector< unsigned >()) | |
virtual | ~AbstractCellPopulation () |
void | InitialiseCells () |
void | SetDataOnAllCells (const std::string &rDataName, double dataValue) |
AbstractMesh< ELEMENT_DIM, SPACE_DIM > & | rGetMesh () |
virtual bool | IsPdeNodeAssociatedWithNonApoptoticCell (unsigned pdeNodeIndex) |
std::list< CellPtr > & | rGetCells () |
std::vector< unsigned > | GetCellMutationStateCount () |
std::vector< unsigned > | GetCellProliferativeTypeCount () |
std::vector< unsigned > | GetCellCyclePhaseCount () |
unsigned | GetNumRealCells () |
unsigned | GetNumAllCells () |
void | SetCellAncestorsToLocationIndices () |
std::set< unsigned > | GetCellAncestors () |
virtual CellPtr | GetCellUsingLocationIndex (unsigned index) |
std::set< CellPtr > | GetCellsUsingLocationIndex (unsigned index) |
virtual bool | IsCellAttachedToLocationIndex (unsigned index) |
void | SetCellUsingLocationIndex (unsigned index, CellPtr pCell) |
virtual void | AddCellUsingLocationIndex (unsigned index, CellPtr pCell) |
virtual void | RemoveCellUsingLocationIndex (unsigned index, CellPtr pCell) |
void | MoveCellInLocationMap (CellPtr pCell, unsigned old_index, unsigned new_index) |
unsigned | GetLocationIndexUsingCell (CellPtr pCell) |
boost::shared_ptr< CellPropertyRegistry > | GetCellPropertyRegistry () |
void | SetDefaultCellMutationStateAndProliferativeTypeOrdering () |
virtual std::set< std::pair< unsigned, unsigned > > | GetNeighbouringEdgeIndices (CellPtr pCell, unsigned pEdgeIndex) |
c_vector< double, SPACE_DIM > | GetCentroidOfCellPopulation () |
virtual void | UpdateCellProcessLocation () |
virtual void | CloseWritersFiles () |
std::vector< std::string > | GetDivisionsInformation () |
void | AddDivisionInformation (std::string divisionInformation) |
void | ClearDivisionsInformation () |
std::vector< std::string > | GetRemovalsInformation () |
void | AddRemovalInformation (std::string removalInformation) |
void | ClearRemovalsInformation () |
void | GenerateRemovalInformation (CellPtr pCell, std::string killerInfo) |
void | KillCell (CellPtr pCell, std::string killerInfo) |
void | StartApoptosisOnCell (CellPtr pCell, std::string killerInfo) |
void | OutputCellPopulationInfo (out_stream &rParamsFile) |
virtual void | SimulationSetupHook (AbstractCellBasedSimulation< ELEMENT_DIM, SPACE_DIM > *pSimulation) |
bool | GetOutputResultsForChasteVisualizer () |
template<template< unsigned, unsigned > class T> | |
void | AddPopulationWriter () |
template<template< unsigned, unsigned > class T> | |
void | AddCellWriter () |
template<template< unsigned, unsigned > class T> | |
void | AddCellPopulationCountWriter () |
template<template< unsigned, unsigned > class T> | |
void | AddCellPopulationEventWriter () |
void | AddPopulationWriter (boost::shared_ptr< AbstractCellPopulationWriter< ELEMENT_DIM, SPACE_DIM > > pPopulationWriter) |
void | AddCellWriter (boost::shared_ptr< AbstractCellWriter< ELEMENT_DIM, SPACE_DIM > > pCellWriter) |
void | AddCellPopulationCountWriter (boost::shared_ptr< AbstractCellPopulationCountWriter< ELEMENT_DIM, SPACE_DIM > > pCellPopulationCountWriter) |
void | AddCellPopulationEventWriter (boost::shared_ptr< AbstractCellPopulationEventWriter< ELEMENT_DIM, SPACE_DIM > > pCellPopulationEventWriter) |
template<template< unsigned, unsigned > class T> | |
bool | HasWriter () const |
void | SetOutputResultsForChasteVisualizer (bool outputResultsForChasteVisualizer) |
c_vector< double, SPACE_DIM > | GetSizeOfCellPopulation () |
virtual bool | IsRoomToDivide (CellPtr pCell) |
std::pair< unsigned, unsigned > | CreateOrderedPair (unsigned index1, unsigned index2) |
Iterator | Begin () |
Iterator | End () |
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virtual | ~Identifiable () |
std::string | GetIdentifier () const |
Protected Member Functions | |
virtual void | UpdateGhostNodesAfterReMesh (NodeMap &rMap) |
virtual void | Validate () |
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AbstractCentreBasedCellPopulation (AbstractMesh< ELEMENT_DIM, SPACE_DIM > &rMesh) | |
virtual void | AcceptCellWritersAcrossPopulation () |
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AbstractOffLatticeCellPopulation (AbstractMesh< ELEMENT_DIM, SPACE_DIM > &rMesh) | |
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AbstractCellPopulation (AbstractMesh< ELEMENT_DIM, SPACE_DIM > &rMesh) | |
Private Member Functions | |
template<class Archive > | |
void | serialize (Archive &archive, const unsigned int version) |
Friends | |
class | TestMeshBasedCellPopulation |
class | boost::serialization::access |
A facade class encapsulating a mesh-based 'cell population'.
Contains a group of cells and maintains the associations between cells and nodes in the mesh.
ELEMENT_DIM | Dimension of the elements. |
SPACE_DIM | Dimension of the space. If not specified, it defaults to ELEMENT_DIM. |
Definition at line 64 of file MeshBasedCellPopulation.hpp.
MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::MeshBasedCellPopulation | ( | MutableMesh< ELEMENT_DIM, SPACE_DIM > & | rMesh, |
std::vector< CellPtr > & | rCells, | ||
const std::vector< unsigned > | locationIndices = {} , |
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bool | deleteMesh = false , |
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bool | validate = true |
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Create a new cell population facade from a mesh and collection of cells.
There must be precisely 1 cell for each node of the mesh.
rMesh | a mutable tetrahedral mesh |
rCells | cells corresponding to the nodes of the mesh |
locationIndices | an optional vector of location indices that correspond to real cells |
deleteMesh | set to true if you want the cell population to free the mesh memory on destruction |
validate | whether to validate the cell population |
Definition at line 52 of file MeshBasedCellPopulation.cpp.
References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mCells, MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mpMutableMesh, AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mrMesh, MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::rGetMesh(), and MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::Validate().
MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::MeshBasedCellPopulation | ( | MutableMesh< ELEMENT_DIM, SPACE_DIM > & | rMesh | ) |
Constructor for use by the de-serializer.
rMesh | a mutable tetrahedral mesh. |
Definition at line 88 of file MeshBasedCellPopulation.cpp.
References MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mDeleteMesh, MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mpMutableMesh, MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mpVoronoiTessellation, and AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mrMesh.
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Destructor.
Definition at line 97 of file MeshBasedCellPopulation.cpp.
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A virtual method to accept a cell writer so it can write data from this object to file.
pCellWriter | the population writer. |
pCell | the cell whose data are being written. |
Implements AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >.
Definition at line 614 of file MeshBasedCellPopulation.cpp.
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A virtual method to accept a cell population count writer so it can write data from this object to file.
pPopulationCountWriter | the population count writer. |
Implements AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >.
Definition at line 602 of file MeshBasedCellPopulation.cpp.
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A virtual method to accept a cell population event writer so it can write data from this object to file.
pPopulationEventWriter | the population event writer. |
Implements AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >.
Definition at line 608 of file MeshBasedCellPopulation.cpp.
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A virtual method to accept a cell population writer so it can write data from this object to file.
pPopulationWriter | the population writer. |
Implements AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >.
Definition at line 596 of file MeshBasedCellPopulation.cpp.
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Overridden AddCell() method.
Add a new cell to the cell population and update mIsGhostNode.
pNewCell | the cell to add |
pParentCell | pointer to a parent cell - this is required for mesh-based cell populations |
Reimplemented from AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >.
Reimplemented in MeshBasedCellPopulationWithGhostNodes< DIM >.
Definition at line 549 of file MeshBasedCellPopulation.cpp.
Referenced by MeshBasedCellPopulationWithGhostNodes< DIM >::AddCell().
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Overridden AddNode() method.
Add a new node to the cell population.
pNewNode | pointer to the new node |
Implements AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_DIM >.
Definition at line 128 of file MeshBasedCellPopulation.cpp.
void MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::CalculateRestLengths | ( | ) |
Populate mSpringRestLengths by looping over all springs and calculating the current length
Definition at line 1240 of file MeshBasedCellPopulation.cpp.
References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::CreateOrderedPair(), Node< SPACE_DIM >::GetIndex(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mHasVariableRestLength, MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mSpringRestLengths, MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::rGetMesh(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::SpringsBegin(), and MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::SpringsEnd().
void MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::CheckCellPointers | ( | ) |
Helper method for use in debugging.
Definition at line 1087 of file MeshBasedCellPopulation.cpp.
References AbstractCellCycleModel::GetCell(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetCellUsingLocationIndex(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetLocationIndexUsingCell(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mCells, AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mMarkedSprings, and UNUSED_OPT.
void MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::CreateVoronoiTessellation | ( | ) |
Create a Voronoi tessellation of the mesh.
Definition at line 906 of file MeshBasedCellPopulation.cpp.
References NEVER_REACHED.
Referenced by DivisionBiasTrackingModifier< DIM >::UpdateCellData(), VolumeTrackingModifier< DIM >::UpdateCellData(), and HeterotypicBoundaryLengthWriter< ELEMENT_DIM, SPACE_DIM >::Visit().
void MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::DivideLongSprings | ( | double | springDivisionThreshold | ) |
Divides springs longer than the given threshold
springDivisionThreshold | a given threshold |
Definition at line 461 of file MeshBasedCellPopulation.cpp.
double MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetAreaBasedDampingConstantParameter | ( | ) |
Definition at line 1167 of file MeshBasedCellPopulation.cpp.
References MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mAreaBasedDampingConstantParameter.
double MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetBoundedVoroniTesselationLengthCutoff | ( | ) |
Definition at line 872 of file MeshBasedCellPopulation.cpp.
bool MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetBoundVoronoiTessellation | ( | ) |
Definition at line 847 of file MeshBasedCellPopulation.cpp.
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Overridden GetDampingConstant() method that includes the case of a cell-area-based damping constant.
nodeIndex | the global index of this node |
We use a linear dependence of the form
new_damping_const = old_damping_const * (d0+d1*A)
where d0, d1 are parameters, A is the cell's area, and old_damping_const is the damping constant if not using mUseAreaBasedDampingConstant
Compute the parameter d1 such that d0+A*d1=1, where A is the equilibrium area of a cell (this is equal to sqrt(3.0)/4, which is a third of the area of a regular hexagon of edge length 1)
The cell area should not be too large - the next assertion is to avoid getting an infinite cell area, which may occur if area-based viscosity is chosen in the absence of ghost nodes.
Reimplemented from AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >.
Definition at line 140 of file MeshBasedCellPopulation.cpp.
References AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetDampingConstant().
Referenced by NodeVelocityWriter< ELEMENT_DIM, SPACE_DIM >::Visit().
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Overridden GetNeighbouringNodeIndices() method.
index | the node index |
Implements AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >.
Definition at line 1211 of file MeshBasedCellPopulation.cpp.
References Node< SPACE_DIM >::ContainingElementsBegin(), Node< SPACE_DIM >::ContainingElementsEnd(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetElement(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNodeGlobalIndex(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), and AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mrMesh.
Referenced by DiscreteSystemForceCalculator::CalculateFtAndFn(), DiscreteSystemForceCalculator::GetSamplingAngles(), and HeterotypicBoundaryLengthWriter< ELEMENT_DIM, SPACE_DIM >::Visit().
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Overridden GetNode() method.
index | global index of the specified Node |
Implements AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >.
Definition at line 532 of file MeshBasedCellPopulation.cpp.
Referenced by CellPopulationElementWriter< ELEMENT_DIM, SPACE_DIM >::Visit().
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Overridden GetNumNodes() method.
Implements AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >.
Definition at line 538 of file MeshBasedCellPopulation.cpp.
Referenced by DiscreteSystemForceCalculator::CalculateExtremalNormalForces(), and CellwiseDataGradient< DIM >::SetupGradients().
bool MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetOffsetNewBoundaryNodes | ( | ) |
Definition at line 884 of file MeshBasedCellPopulation.cpp.
double MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetRestLength | ( | unsigned | indexA, |
unsigned | indexB | ||
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indexA | index of first node in pair |
indexB | index of second node in pair |
Definition at line 1268 of file MeshBasedCellPopulation.cpp.
References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::CreateOrderedPair(), EXCEPTION, MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mHasVariableRestLength, and MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mSpringRestLengths.
bool MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetScaleBoundByEdgeLength | ( | ) |
Definition at line 859 of file MeshBasedCellPopulation.cpp.
double MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetSurfaceAreaOfVoronoiElement | ( | unsigned | index | ) |
This method should be called instead of calling GetVoronoiTessellation()->GetSurfaceAreaOfElement() because the global indices of Delaunay nodes and Voronoi elements may not match, e.g. if a node is a ghost node or corresponds to a Voronoi face.
index | a node global index |
Definition at line 1062 of file MeshBasedCellPopulation.cpp.
References MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mpVoronoiTessellation.
Referenced by LinearSpringWithVariableSpringConstantsForce< DIM >::VariableSpringConstantMultiplicationFactor().
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Overridden GetTetrahedralMeshForPdeModifier() method.
This method is called by AbstractGrowingDomainPdeModifier.
Implements AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >.
Reimplemented in MeshBasedCellPopulationWithGhostNodes< DIM >.
Definition at line 224 of file MeshBasedCellPopulation.cpp.
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Overridden GetVolumeOfCell() method.
pCell | boost shared pointer to a cell |
Implements AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >.
Definition at line 765 of file MeshBasedCellPopulation.cpp.
References AbstractTetrahedralElement< ELEMENT_DIM, SPACE_DIM >::CalculateJacobian(), Node< SPACE_DIM >::ContainingElementsBegin(), Node< SPACE_DIM >::ContainingElementsEnd(), AbstractTetrahedralElement< ELEMENT_DIM, SPACE_DIM >::GetVolume(), NEVER_REACHED, and Node< SPACE_DIM >::rGetContainingElementIndices().
double MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetVolumeOfVoronoiElement | ( | unsigned | index | ) |
This method should be called instead of calling GetVoronoiTessellation()->GetVolumeOfElement() because the global indices of Delaunay nodes and Voronoi elements may not match, e.g. if a node is a ghost node or corresponds to a Voronoi face.
index | a node global index |
Definition at line 1054 of file MeshBasedCellPopulation.cpp.
References MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mpVoronoiTessellation.
double MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetVoronoiEdgeLength | ( | unsigned | index1, |
unsigned | index2 | ||
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This method should be called instead of calling GetVoronoiTessellation()->GetEdgeLength() because the global indices of Delaunay nodes and Voronoi elements may not match, e.g. if a node is a ghost node or corresponds to a Voronoi face.
index1 | a node global index |
index2 | a node global index |
Definition at line 1070 of file MeshBasedCellPopulation.cpp.
References EXCEPTION, and MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mpVoronoiTessellation.
Referenced by LinearSpringWithVariableSpringConstantsForce< DIM >::VariableSpringConstantMultiplicationFactor(), and HeterotypicBoundaryLengthWriter< ELEMENT_DIM, SPACE_DIM >::Visit().
VertexMesh< ELEMENT_DIM, SPACE_DIM > * MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetVoronoiTessellation | ( | ) |
Definition at line 1047 of file MeshBasedCellPopulation.cpp.
References MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mpVoronoiTessellation.
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Overridden GetWidth() method.
Calculate the 'width' of any dimension of the cell population by calling GetWidth() on the mesh.
rDimension | a dimension (0,1 or 2) |
Implements AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >.
Definition at line 1203 of file MeshBasedCellPopulation.cpp.
References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mrMesh.
bool MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetWriteVtkAsPoints | ( | ) |
Definition at line 835 of file MeshBasedCellPopulation.cpp.
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Overridden OpenWritersFiles() method.
Open all files in mCellPopulationWriters and mCellWriters for writing (not appending).
rOutputFileHandler | handler for the directory in which to open this file. |
Reimplemented from AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >.
Reimplemented in MeshBasedCellPopulationWithGhostNodes< DIM >.
Definition at line 571 of file MeshBasedCellPopulation.cpp.
Referenced by MeshBasedCellPopulationWithGhostNodes< DIM >::OpenWritersFiles().
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Outputs CellPopulation parameters to file
rParamsFile | the file stream to which the parameters are output |
Reimplemented from AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >.
Reimplemented in MeshBasedCellPopulationWithGhostNodes< DIM >.
Definition at line 1190 of file MeshBasedCellPopulation.cpp.
References MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mAreaBasedDampingConstantParameter, MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mBoundVoronoiTessellation, MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mHasVariableRestLength, MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mUseAreaBasedDampingConstant, MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mWriteVtkAsPoints, and AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::OutputCellPopulationParameters().
Referenced by MeshBasedCellPopulationWithGhostNodes< DIM >::OutputCellPopulationParameters().
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Remove all cells that are labelled as dead.
Note that this now calls MutableMesh::DeleteNodePriorToReMesh() and therefore a ReMesh(map) must be called before any element information is used.
Note also that after calling this method the cell population will be in an inconsistent state until Update() is called! So don't try iterating over cells or anything like that.
Implements AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >.
Definition at line 230 of file MeshBasedCellPopulation.cpp.
MutableMesh< ELEMENT_DIM, SPACE_DIM > & MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::rGetMesh | ( | ) |
Definition at line 212 of file MeshBasedCellPopulation.cpp.
Referenced by MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::MeshBasedCellPopulation(), DiscreteSystemForceCalculator::CalculateFtAndFn(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::CalculateRestLengths(), CryptStatistics::CellIsInSection(), CryptStatistics::CellIsInSectionPeriodic(), CryptStatistics::GetCryptSection(), DiscreteSystemForceCalculator::GetSamplingAngles(), CellwiseDataGradient< DIM >::SetupGradients(), BoundaryNodeWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), CellPopulationElementWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), NodeLocationWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), NodeVelocityWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), and DiscreteSystemForceCalculator::WriteResultsToFile().
const MutableMesh< ELEMENT_DIM, SPACE_DIM > & MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::rGetMesh | ( | ) | const |
Definition at line 218 of file MeshBasedCellPopulation.cpp.
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Overridden rGetNodePairs method which uses the Delaunay triangulatiuon
Implements AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >.
Definition at line 1181 of file MeshBasedCellPopulation.cpp.
References MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mNodePairs, and NEVER_REACHED.
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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.
archive | the archive |
version | the current version of this class |
Definition at line 82 of file MeshBasedCellPopulation.hpp.
References MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mAreaBasedDampingConstantParameter, MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mBoundedVoroniTesselationLengthCutoff, MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mBoundVoronoiTessellation, MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mHasVariableRestLength, MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mOffsetNewBoundaryNodes, MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mpVoronoiTessellation, MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mScaleBoundByEdgeLength, MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mSpringRestLengths, MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mUseAreaBasedDampingConstant, MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mWriteVtkAsPoints, and MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::Validate().
void MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::SetAreaBasedDampingConstant | ( | bool | useAreaBasedDampingConstant | ) |
Set method for mUseAreaBasedDampingConstant.
useAreaBasedDampingConstant | whether to use a viscosity that is linear in the cell area, rather than constant |
Definition at line 114 of file MeshBasedCellPopulation.cpp.
References NEVER_REACHED.
void MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::SetAreaBasedDampingConstantParameter | ( | double | areaBasedDampingConstantParameter | ) |
Set mAreaBasedDampingConstantParameter.
areaBasedDampingConstantParameter | the new value of mAreaBasedDampingConstantParameter |
Definition at line 1173 of file MeshBasedCellPopulation.cpp.
References MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mAreaBasedDampingConstantParameter.
void MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::SetBoundedVoroniTesselationLengthCutoff | ( | double | boundedVoroniTesselationLengthCutoff | ) |
Set mBoundedVoroniTesselationLengthCutoff.
boundedVoroniTesselationLengthCutoff | whether to scale the bound with edge lenght in the Voronoi Tesselation. |
Definition at line 865 of file MeshBasedCellPopulation.cpp.
void MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::SetBoundVoronoiTessellation | ( | bool | boundVoronoiTessellation | ) |
Set mBoundVoronoiTessellation.
boundVoronoiTessellation | whether to bound the Voronoi Tesselation. |
Definition at line 841 of file MeshBasedCellPopulation.cpp.
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Overridden SetNode() method.
Move the node with a given index to a new point in space.
nodeIndex | the index of the node to be moved |
rNewLocation | the new target location of the node |
Implements AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_DIM >.
Definition at line 134 of file MeshBasedCellPopulation.cpp.
References MutableMesh< ELEMENT_DIM, SPACE_DIM >::SetNode().
void MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::SetOffsetNewBoundaryNodes | ( | bool | offsetNewBoundaryNodes | ) |
Set mOffsetNewBoundaryNodes.
offsetNewBoundaryNodes | whether to add new nodes towards the centre of the boundary edges for the bounded voronoi tesselation. |
Definition at line 878 of file MeshBasedCellPopulation.cpp.
void MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::SetRestLength | ( | unsigned | indexA, |
unsigned | indexB, | ||
double | restLength | ||
) |
Helper method to modify the rest length of a given spring
indexA | index of first node in pair |
indexB | index of second node in pair |
restLength | the new rest length |
Definition at line 1292 of file MeshBasedCellPopulation.cpp.
References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::CreateOrderedPair(), EXCEPTION, MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mHasVariableRestLength, and MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mSpringRestLengths.
void MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::SetScaleBoundByEdgeLength | ( | bool | scaleBoundByEdgeLength | ) |
Set mScaleBoundByEdgeLength.
scaleBoundByEdgeLength | whether to scale the bound with edge lenght in the Voronoi Tesselation. |
Definition at line 853 of file MeshBasedCellPopulation.cpp.
void MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::SetWriteVtkAsPoints | ( | bool | writeVtkAsPoints | ) |
Set mWriteVtkAsPoints.
writeVtkAsPoints | whether to write cells as points in VTK |
Definition at line 829 of file MeshBasedCellPopulation.cpp.
MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::SpringIterator MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::SpringsBegin | ( | ) |
Definition at line 1035 of file MeshBasedCellPopulation.cpp.
References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mrMesh.
Referenced by CryptProjectionForce::AddForceContribution(), LinearSpringWithVariableSpringConstantsForce< DIM >::AddForceContribution(), AbstractTwoBodyInteractionForce< ELEMENT_DIM, SPACE_DIM >::AddForceContribution(), and MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::CalculateRestLengths().
MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::SpringIterator MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::SpringsEnd | ( | ) |
Definition at line 1041 of file MeshBasedCellPopulation.cpp.
References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mrMesh.
Referenced by CryptProjectionForce::AddForceContribution(), LinearSpringWithVariableSpringConstantsForce< DIM >::AddForceContribution(), AbstractTwoBodyInteractionForce< ELEMENT_DIM, SPACE_DIM >::AddForceContribution(), and MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::CalculateRestLengths().
void MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::TessellateIfNeeded | ( | ) |
Tessellates when required: if areas or volumes are needed for mUseAreaBasedDampingConstant; if a CellPopulationAreaWriter or CellVolumesWriter has been added to the population; or if Voronoi data are to be output.
Definition at line 444 of file MeshBasedCellPopulation.cpp.
References GenericEventHandler< 11, CellBasedEventHandler >::BeginEvent().
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Overridden Update(bool hasHadBirthsOrDeaths) method. Fixes up the mappings between cells and nodes.
hasHadBirthsOrDeaths | - a bool saying whether cell population has had Births Or Deaths not needed in this cell population class |
If node radii are set, then we must keep a record of these, since they will be cleared during the remeshing process. We then restore these attributes to the nodes after calling ReMesh().
At present, we check whether node radii are set by interrogating the radius of the first node in the mesh and asking if it is strictly greater than zero (the default value, as set in the NodeAttributes constructor). Hence, we assume that either ALL node radii are set, or NONE are.
Implements AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >.
Definition at line 289 of file MeshBasedCellPopulation.cpp.
Referenced by CellPopulationAdjacencyMatrixWriter< ELEMENT_DIM, SPACE_DIM >::Visit().
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Update mIsGhostNode if required by a remesh.
rMap | A map between node indices before and after remesh |
Reimplemented in MeshBasedCellPopulationWithGhostNodes< DIM >.
Definition at line 544 of file MeshBasedCellPopulation.cpp.
bool MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::UseAreaBasedDampingConstant | ( | ) |
Definition at line 108 of file MeshBasedCellPopulation.cpp.
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Check consistency of our internal data structures. Each node must have a cell associated with it.
Implements AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >.
Reimplemented in MeshBasedCellPopulationWithGhostNodes< DIM >.
Definition at line 192 of file MeshBasedCellPopulation.cpp.
Referenced by MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::MeshBasedCellPopulation(), and MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::serialize().
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Overridden WriteDataToVisualizerSetupFile() method. Write any data necessary to a visualization setup file. Used by AbstractCellBasedSimulation::WriteVisualizerSetupFile().
pVizSetupFile | a visualization setup file |
Reimplemented from AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >.
Definition at line 892 of file MeshBasedCellPopulation.cpp.
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Overridden WriteResultsToFiles() method.
rDirectory | pathname of the output directory, relative to where Chaste output is stored |
Reimplemented from AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >.
Definition at line 585 of file MeshBasedCellPopulation.cpp.
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Overridden WriteVtkResultsToFile() method.
rDirectory | pathname of the output directory, relative to where Chaste output is stored |
Implements AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >.
Reimplemented in MeshBasedCellPopulationWithGhostNodes< DIM >.
Definition at line 620 of file MeshBasedCellPopulation.cpp.
Needed for serialization.
Definition at line 69 of file MeshBasedCellPopulation.hpp.
Definition at line 66 of file MeshBasedCellPopulation.hpp.
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Non-dimensional parameter d0 for use in area-based damping constant calculations.
Definition at line 141 of file MeshBasedCellPopulation.hpp.
Referenced by MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetAreaBasedDampingConstantParameter(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::OutputCellPopulationParameters(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::serialize(), and MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::SetAreaBasedDampingConstantParameter().
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Edges longer than this are ignored in boundary calculation for the bounded voronio tesselation.
Definition at line 153 of file MeshBasedCellPopulation.hpp.
Referenced by MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::serialize().
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Whether to bound the voronoi tesselation to avoid infinite cells on boundary.
Definition at line 147 of file MeshBasedCellPopulation.hpp.
Referenced by MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::OutputCellPopulationParameters(), and MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::serialize().
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Whether to delete the mesh when we are destroyed. Needed if this cell population has been de-serialized.
Definition at line 130 of file MeshBasedCellPopulation.hpp.
Referenced by MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::MeshBasedCellPopulation().
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Whether springs have variable rest lengths.
Definition at line 159 of file MeshBasedCellPopulation.hpp.
Referenced by MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::CalculateRestLengths(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetRestLength(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::OutputCellPopulationParameters(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::serialize(), and MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::SetRestLength().
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Node pairs for force calculations.
Definition at line 162 of file MeshBasedCellPopulation.hpp.
Referenced by MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::rGetNodePairs().
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whether to add new nodes towards the centre of the boundary edges for the bounded voronoi tesselation.
Definition at line 156 of file MeshBasedCellPopulation.hpp.
Referenced by MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::serialize().
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Static cast of the mesh from AbstractCellPopulation
Definition at line 124 of file MeshBasedCellPopulation.hpp.
Referenced by MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::MeshBasedCellPopulation(), and MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::MeshBasedCellPopulation().
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Pointer to a VertexMesh object that stores the Voronoi tessellation that is dual to mrMesh. The tessellation is created by calling CreateVoronoiTessellation() and can be accessed by calling GetVoronoiTessellation().
The tessellation can be used to compute the area and perimeter (in 2D) or volume and surface area (in 3D) of the Voronoi element corresponding to each node in the Delaunay mesh (including ghost nodes) by calling the methods GetVolumeOfVoronoiElement() and GetSurfaceAreaOfVoronoiElement() respectively. Each of these methods should be called rather than the relevant method on the VertexMesh. This is because the index of a given Node in mrMesh may not equal the index of the corresponding VertexElement in mpVoronoiTessellation; a map between these indices may be accessed by calling the methods GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex() and GetVoronoiElementIndexCorrespondingToDelaunayNodeIndex() on mpVoronoiTessellation.
Definition at line 121 of file MeshBasedCellPopulation.hpp.
Referenced by MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::MeshBasedCellPopulation(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetSurfaceAreaOfVoronoiElement(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetVolumeOfVoronoiElement(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetVoronoiEdgeLength(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetVoronoiTessellation(), and MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::serialize().
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Whether to scale the bound by edge lenght when using the bounded voronoi tesselation.
Definition at line 150 of file MeshBasedCellPopulation.hpp.
Referenced by MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::serialize().
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Keeps track of the rest lengths of springs if these are being used in the simulation.
Definition at line 135 of file MeshBasedCellPopulation.hpp.
Referenced by MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::CalculateRestLengths(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetRestLength(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::serialize(), and MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::SetRestLength().
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Whether to use a viscosity that is linear in the cell area, rather than constant.
Definition at line 138 of file MeshBasedCellPopulation.hpp.
Referenced by MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::OutputCellPopulationParameters(), and MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::serialize().
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Whether to write cells as points in VTK.
Definition at line 144 of file MeshBasedCellPopulation.hpp.
Referenced by MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::OutputCellPopulationParameters(), and MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::serialize().