#include <MeshBasedCellPopulation.hpp>
Inheritance diagram for MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >:
Collaboration diagram for MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >:
Detailed Description
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>
class MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >
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.
Definition at line 59 of file MeshBasedCellPopulation.hpp.
Constructor & Destructor Documentation
| MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::MeshBasedCellPopulation | ( | MutableMesh< ELEMENT_DIM, SPACE_DIM > & | rMesh, |
| std::vector< CellPtr > & | rCells, | ||
| const std::vector< unsigned > | locationIndices = std::vector<unsigned>(), |
||
| bool | deleteMesh = false, |
||
| bool | validate = true |
||
| ) |
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.
- Parameters:
-
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 46 of file MeshBasedCellPopulation.cpp.
References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mCells, MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mpMutableMesh, AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mrMesh, 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.
- Parameters:
-
rMesh a mutable tetrahedral mesh.
Definition at line 72 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.
| MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::~MeshBasedCellPopulation | ( | ) | [virtual] |
Destructor.
Definition at line 81 of file MeshBasedCellPopulation.cpp.
Member Function Documentation
| CellPtr MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::AddCell | ( | CellPtr | pNewCell, |
| const c_vector< double, SPACE_DIM > & | rCellDivisionVector, | ||
| CellPtr | pParentCell | ||
| ) | [virtual] |
Overridden AddCell() method.
Add a new cell to the cell population and update mIsGhostNode.
- Parameters:
-
pNewCell the cell to add rCellDivisionVector the position in space at which to put it pParentCell pointer to a parent cell - this is required for mesh-based cell populations
- Returns:
- address of cell as it appears in the cell list (internal of this method uses a copy constructor along the way)
Reimplemented from AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >.
Definition at line 359 of file MeshBasedCellPopulation.cpp.
References AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::AddCell().
Referenced by MeshBasedCellPopulationWithGhostNodes< DIM >::AddCell().
| unsigned MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::AddNode | ( | Node< SPACE_DIM > * | pNewNode | ) | [virtual] |
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
Implements AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_DIM >.
Definition at line 105 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 1231 of file MeshBasedCellPopulation.cpp.
References Node< SPACE_DIM >::GetIndex(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mHasVariableRestLength, MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mSpringRestLengths, Node< SPACE_DIM >::rGetLocation(), 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 1058 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, and AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mMarkedSprings.
| void MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::CloseOutputFiles | ( | ) | [virtual] |
Overridden CloseOutputFiles() method.
Reimplemented from AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >.
Definition at line 399 of file MeshBasedCellPopulation.cpp.
References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::CloseOutputFiles().
| void MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::CreateOutputFiles | ( | const std::string & | rDirectory, |
| bool | cleanOutputDirectory | ||
| ) | [virtual] |
Overridden CreateOutputFiles() method.
- Parameters:
-
rDirectory pathname of the output directory, relative to where Chaste output is stored cleanOutputDirectory whether to delete the contents of the output directory prior to output file creation
Reimplemented from AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >.
Definition at line 381 of file MeshBasedCellPopulation.cpp.
References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::CreateOutputFiles(), and OutputFileHandler::OpenOutputFile().
| void MeshBasedCellPopulation< 2, 3 >::CreateVoronoiTessellation | ( | ) |
Can't tessellate 2d meshes in 3d space yet.
Definition at line 966 of file MeshBasedCellPopulation.cpp.
References NEVER_REACHED.
| void MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::CreateVoronoiTessellation | ( | ) |
Create a Voronoi tessellation of the mesh.
Referenced by VolumeTrackedOffLatticeSimulation< DIM >::UpdateCellData().
| void MeshBasedCellPopulation< 3 >::CreateVoronoiTessellation | ( | ) |
The cylindrical mesh is only defined in 2D, hence there is a separate definition for this method in 3D, which doesn't have the capability of dealing with periodic boundaries in 3D. This is /todo #1374.
Definition at line 978 of file MeshBasedCellPopulation.cpp.
References MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mpVoronoiTessellation, and AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mrMesh.
| void MeshBasedCellPopulation< 1, 1 >::CreateVoronoiTessellation | ( | ) |
The VoronoiTessellation class is only defined in 2D or 3D, hence there are two definitions to this method (one templated and one not).
Definition at line 989 of file MeshBasedCellPopulation.cpp.
References NEVER_REACHED.
| void MeshBasedCellPopulation< 1, 2 >::CreateVoronoiTessellation | ( | ) |
The VoronoiTessellation class is only defined in 2D or 3D, hence there are two definitions to this method (one templated and one not).
Definition at line 1000 of file MeshBasedCellPopulation.cpp.
References NEVER_REACHED.
| void MeshBasedCellPopulation< 1, 3 >::CreateVoronoiTessellation | ( | ) |
The VoronoiTessellation class is only defined in 2D or 3D, hence there are two definitions to this method (one templated and one not).
Definition at line 1011 of file MeshBasedCellPopulation.cpp.
References NEVER_REACHED.
| double MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetAreaBasedDampingConstantParameter | ( | ) |
- Returns:
- mAreaBasedDampingConstantParameter
Definition at line 1137 of file MeshBasedCellPopulation.cpp.
References MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mAreaBasedDampingConstantParameter.
| double MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetDampingConstant | ( | unsigned | nodeIndex | ) | [virtual] |
Overridden GetDampingConstant() method that includes the case of a cell-area-based damping constant.
- Parameters:
-
nodeIndex the global index of this node
- Returns:
- the damping constant for the given Cell.
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)/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 117 of file MeshBasedCellPopulation.cpp.
References AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetDampingConstant().
| std::set< unsigned > MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetNeighbouringNodeIndices | ( | unsigned | index | ) | [virtual] |
Overridden GetNeighbouringNodeIndices() method.
- Parameters:
-
index the node index
- Returns:
- the set of neighbouring node indices.
Implements AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >.
Definition at line 1202 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(), and DiscreteSystemForceCalculator::GetSamplingAngles().
| Node< SPACE_DIM > * MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetNode | ( | unsigned | index | ) | [virtual] |
Overridden GetNode() method.
- Parameters:
-
index global index of the specified Node
- Returns:
- pointer to the Node with given index.
Implements AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >.
Definition at line 342 of file MeshBasedCellPopulation.cpp.
| unsigned MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetNumNodes | ( | ) | [virtual] |
Overridden GetNumNodes() method.
- Returns:
- the number of nodes in the cell population.
Implements AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >.
Definition at line 348 of file MeshBasedCellPopulation.cpp.
Referenced by DiscreteSystemForceCalculator::CalculateExtremalNormalForces(), and CellwiseDataGradient< DIM >::SetupGradients().
| bool MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetOutputCellPopulationVolumes | ( | ) |
- Returns:
- mOutputCellPopulationVolumes
Definition at line 1162 of file MeshBasedCellPopulation.cpp.
References MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mOutputCellPopulationVolumes.
| bool MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetOutputVoronoiData | ( | ) |
- Returns:
- mOutputVoronoiData
Definition at line 1150 of file MeshBasedCellPopulation.cpp.
References MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mOutputVoronoiData.
| double MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetRestLength | ( | unsigned | indexA, |
| unsigned | indexB | ||
| ) |
Return the rest length for a given spring
- Parameters:
-
indexA index of first node in pair indexB index of second node in pair
- Todo:
- #2110 This code is not covered by any tests
Definition at line 1261 of file MeshBasedCellPopulation.cpp.
References MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mHasVariableRestLength, MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mSpringRestLengths, and NEVER_REACHED.
| double MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetSurfaceAreaOfVoronoiElement | ( | unsigned | index | ) |
Get the surface area of the element of mpVoronoiTessellation associated with the node with this global index in the Delaunay mesh.
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.
- Parameters:
-
index a node global index
Definition at line 1033 of file MeshBasedCellPopulation.cpp.
References MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mpVoronoiTessellation.
Referenced by LinearSpringWithVariableSpringConstantsForce< DIM >::VariableSpringConstantMultiplicationFactor().
| double MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetVolumeOfCell | ( | CellPtr | pCell | ) | [virtual] |
Overridden GetVolumeOfCell() method.
- Parameters:
-
pCell boost shared pointer to a cell
Implements AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >.
Definition at line 773 of file MeshBasedCellPopulation.cpp.
| double MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetVolumeOfVoronoiElement | ( | unsigned | index | ) |
Get the volume (or area in 2D, or length in 1D) of the element of mpVoronoiTessellation associated with the node with this global index in the Delaunay mesh.
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.
- Todo:
- This method is somewhat redundant following the introduction of the method GetVolumeOfCell() (see #1985).
- Parameters:
-
index a node global index
Definition at line 1025 of file MeshBasedCellPopulation.cpp.
References MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mpVoronoiTessellation.
| double MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetVoronoiEdgeLength | ( | unsigned | index1, |
| unsigned | index2 | ||
| ) |
Get the length of the edge of mpVoronoiTessellation associated with the two nodes with these global indices in the Delaunay mesh.
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.
- Parameters:
-
index1 a node global index index2 a node global index
Definition at line 1041 of file MeshBasedCellPopulation.cpp.
References EXCEPTION, and MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mpVoronoiTessellation.
Referenced by LinearSpringWithVariableSpringConstantsForce< DIM >::VariableSpringConstantMultiplicationFactor().
| VertexMesh< ELEMENT_DIM, SPACE_DIM > * MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetVoronoiTessellation | ( | ) |
Get a reference to mpVoronoiTessellation.
Definition at line 1018 of file MeshBasedCellPopulation.cpp.
References MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mpVoronoiTessellation.
| double MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetWidth | ( | const unsigned & | rDimension | ) | [virtual] |
Overridden GetWidth() method.
Calculate the 'width' of any dimension of the cell population by calling GetWidth() on the mesh.
- 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 1194 of file MeshBasedCellPopulation.cpp.
References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mrMesh.
| bool MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetWriteVtkAsPoints | ( | ) |
- Returns:
- mWriteVtkAsPoints.
Definition at line 851 of file MeshBasedCellPopulation.cpp.
| void MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::OutputCellPopulationParameters | ( | out_stream & | rParamsFile | ) | [virtual] |
Outputs CellPopulation parameters to file
- Parameters:
-
rParamsFile the file stream to which the parameters are output
Reimplemented from AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >.
Reimplemented in MeshBasedCellPopulationWithGhostNodes< DIM >.
Definition at line 1182 of file MeshBasedCellPopulation.cpp.
References MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mAreaBasedDampingConstantParameter, MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mOutputCellPopulationVolumes, MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mOutputVoronoiData, and MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mUseAreaBasedDampingConstant.
Referenced by MeshBasedCellPopulationWithGhostNodes< DIM >::OutputCellPopulationParameters().
| unsigned MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::RemoveDeadCells | ( | ) | [virtual] |
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.
- Returns:
- number of cells removed.
Implements AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >.
Definition at line 192 of file MeshBasedCellPopulation.cpp.
References MutableMesh< ELEMENT_DIM, SPACE_DIM >::DeleteNodePriorToReMesh().
| const MutableMesh< ELEMENT_DIM, SPACE_DIM > & MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::rGetMesh | ( | ) | const |
- Returns:
- const reference to mrMesh (used in archiving).
Definition at line 186 of file MeshBasedCellPopulation.cpp.
| MutableMesh< ELEMENT_DIM, SPACE_DIM > & MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::rGetMesh | ( | ) |
- Returns:
- reference to mrMesh.
Reimplemented from AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >.
Definition at line 180 of file MeshBasedCellPopulation.cpp.
Referenced by DiscreteSystemForceCalculator::CalculateFtAndFn(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::CalculateRestLengths(), CryptStatistics::CellIsInSection(), CryptStatistics::CellIsInSectionPeriodic(), CryptStatistics::GetCryptSection(), DiscreteSystemForceCalculator::GetSamplingAngles(), CellwiseDataGradient< DIM >::SetupGradients(), and DiscreteSystemForceCalculator::WriteResultsToFile().
| std::set< std::pair< Node< SPACE_DIM > *, Node< SPACE_DIM > * > > & MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::rGetNodePairs | ( | ) | [virtual] |
Overridden rGetNodePairs method which uses the Delaunay triangulatiuon
- Returns:
- Node pairs for force calculation.
Implements AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >.
Definition at line 1174 of file MeshBasedCellPopulation.cpp.
References MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mNodePairs, and NEVER_REACHED.
| void MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::serialize | ( | Archive & | archive, |
| const unsigned int | version | ||
| ) | [inline, private] |
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.
- Parameters:
-
archive the archive version the current version of this class
Reimplemented from AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >.
Reimplemented in MeshBasedCellPopulationWithGhostNodes< DIM >.
Definition at line 77 of file MeshBasedCellPopulation.hpp.
| void MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::SetAreaBasedDampingConstant | ( | bool | useAreaBasedDampingConstant | ) |
Set method for mUseAreaBasedDampingConstant.
- Parameters:
-
useAreaBasedDampingConstant whether to use a viscosity that is linear in the cell area, rather than constant
Definition at line 98 of file MeshBasedCellPopulation.cpp.
| void MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::SetAreaBasedDampingConstantParameter | ( | double | areaBasedDampingConstantParameter | ) |
Set mAreaBasedDampingConstantParameter.
- Parameters:
-
areaBasedDampingConstantParameter the new value of mAreaBasedDampingConstantParameter
Definition at line 1143 of file MeshBasedCellPopulation.cpp.
References MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mAreaBasedDampingConstantParameter.
| void MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::SetNode | ( | unsigned | nodeIndex, |
| ChastePoint< SPACE_DIM > & | rNewLocation | ||
| ) | [virtual] |
Overridden SetNode() method.
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
Implements AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_DIM >.
Definition at line 111 of file MeshBasedCellPopulation.cpp.
References MutableMesh< ELEMENT_DIM, SPACE_DIM >::SetNode().
| void MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::SetOutputCellPopulationVolumes | ( | bool | outputCellPopulationVolumes | ) |
Set mOutputCellPopulationVolumes.
- Parameters:
-
outputCellPopulationVolumes the new value of mOutputCellPopulationVolumes
Definition at line 1168 of file MeshBasedCellPopulation.cpp.
References MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mOutputCellPopulationVolumes.
| void MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::SetOutputVoronoiData | ( | bool | outputVoronoiData | ) |
Set method for mOutputVoronoiData.
- Parameters:
-
outputVoronoiData whether to output cell area and perimeter information
Definition at line 1156 of file MeshBasedCellPopulation.cpp.
References MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mOutputVoronoiData.
| void MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::SetWriteVtkAsPoints | ( | bool | writeVtkAsPoints | ) |
Set mWriteVtkAsPoints.
- Parameters:
-
writeVtkAsPoints whether to write cells as points in VTK
Definition at line 845 of file MeshBasedCellPopulation.cpp.
| MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::SpringIterator MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::SpringsBegin | ( | ) |
- Returns:
- iterator pointing to the first spring in the cell population
Definition at line 933 of file MeshBasedCellPopulation.cpp.
References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mrMesh.
Referenced by LinearSpringWithVariableSpringConstantsForce< DIM >::AddForceContribution(), CryptProjectionForce::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 | ( | ) |
- Returns:
- iterator pointing to one past the last spring in the cell population
Definition at line 939 of file MeshBasedCellPopulation.cpp.
References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mrMesh.
Referenced by LinearSpringWithVariableSpringConstantsForce< DIM >::AddForceContribution(), CryptProjectionForce::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 or mOutputCellPopulationVolumes or mOutputCellVolumes If Voronoi data is to be output
Definition at line 328 of file MeshBasedCellPopulation.cpp.
References GenericEventHandler< 11, CellBasedEventHandler >::BeginEvent(), and GenericEventHandler< 11, CellBasedEventHandler >::EndEvent().
| void MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::Update | ( | bool | hasHadBirthsOrDeaths = true | ) | [virtual] |
Overridden Update(bool hasHadBirthsOrDeaths) method. Fixes up the mappings between cells and nodes.
- Parameters:
-
hasHadBirthsOrDeaths - a bool saying whether cell population has had Births Or Deaths not needed in this cell population class
Implements AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >.
Definition at line 248 of file MeshBasedCellPopulation.cpp.
References Node< SPACE_DIM >::ContainingElementsBegin(), Node< SPACE_DIM >::ContainingElementsEnd(), NodeMap::GetNewIndex(), NodeMap::IsDeleted(), NodeMap::IsIdentityMap(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::ReMesh(), Node< SPACE_DIM >::rGetContainingElementIndices(), and AbstractMesh< ELEMENT_DIM, SPACE_DIM >::SetMeshHasChangedSinceLoading().
| void MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::UpdateGhostNodesAfterReMesh | ( | NodeMap & | rMap | ) | [protected, virtual] |
Update mIsGhostNode if required by a remesh.
- Parameters:
-
rMap A map between node indices before and after remesh
Reimplemented in MeshBasedCellPopulationWithGhostNodes< DIM >.
Definition at line 354 of file MeshBasedCellPopulation.cpp.
| bool MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::UseAreaBasedDampingConstant | ( | ) |
- Returns:
- mUseAreaBasedDampingConstant.
Definition at line 92 of file MeshBasedCellPopulation.cpp.
| void MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::Validate | ( | ) | [protected, virtual] |
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 160 of file MeshBasedCellPopulation.cpp.
References EXCEPTION.
Referenced by MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::MeshBasedCellPopulation(), and MeshBasedCellPopulation< 2 >::serialize().
| void MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::WriteCellPopulationVolumeResultsToFile | ( | ) |
Write the current total area (in 2D) or volume (in 3D) of mrMesh, and of the set of apoptotic cells in the cell population (using mpVoronoiTessellation), to mpCellPopulationVolumesFile.
Definition at line 731 of file MeshBasedCellPopulation.cpp.
References SimulationTime::GetTime(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetVolume(), and SimulationTime::Instance().
| void MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::WriteCellVolumeResultsToFile | ( | ) | [virtual] |
Overridden WriteCellVolumeResultsToFile() method.
- Todo:
- It would be simpler to merely iterate over the cell population here
Implements AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >.
Definition at line 794 of file MeshBasedCellPopulation.cpp.
References SimulationTime::GetTime(), and SimulationTime::Instance().
| void MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::WriteResultsToFiles | ( | ) | [virtual] |
Overridden WriteResultsToFiles() method.
Reimplemented from AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >.
Definition at line 416 of file MeshBasedCellPopulation.cpp.
References AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetElementIteratorEnd(), SimulationTime::GetTime(), SimulationTime::Instance(), and AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::WriteResultsToFiles().
| void MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::WriteVoronoiResultsToFile | ( | ) |
Write the current index and location of each node in mrMesh (including ghost nodes), as well as the area and perimeter (in 2D) or volume and surface area (in 3D) of its corresponding element in mpVoronoiTessellation, to mpVoronoiFile.
Definition at line 697 of file MeshBasedCellPopulation.cpp.
References SimulationTime::GetTime(), and SimulationTime::Instance().
| void MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::WriteVtkResultsToFile | ( | ) | [virtual] |
Overridden WriteVtkResultsToFile() method.
Implements AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >.
Reimplemented in MeshBasedCellPopulationWithGhostNodes< DIM >.
Definition at line 476 of file MeshBasedCellPopulation.cpp.
References VertexMeshWriter< ELEMENT_DIM, SPACE_DIM >::AddCellData(), NodesOnlyMesh< SPACE_DIM >::ConstructNodesWithoutMesh(), AbstractCellCycleModel::GetCurrentCellCyclePhase(), SimulationTime::GetTimeStepsElapsed(), SimulationTime::Instance(), UNSIGNED_UNSET, and VertexMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteVtkUsingMesh().
Friends And Related Function Documentation
friend class boost::serialization::access [friend] |
Needed for serialization.
Reimplemented from AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >.
Reimplemented in MeshBasedCellPopulationWithGhostNodes< DIM >.
Definition at line 64 of file MeshBasedCellPopulation.hpp.
Member Data Documentation
double MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mAreaBasedDampingConstantParameter [protected] |
Non-dimensional parameter d0 for use in area-based damping constant calculations.
Definition at line 147 of file MeshBasedCellPopulation.hpp.
Referenced by MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetAreaBasedDampingConstantParameter(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::OutputCellPopulationParameters(), MeshBasedCellPopulation< 2 >::serialize(), and MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::SetAreaBasedDampingConstantParameter().
bool MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mDeleteMesh [protected] |
Whether to delete the mesh when we are destroyed. Needed if this cell population has been de-serialized.
Definition at line 127 of file MeshBasedCellPopulation.hpp.
Referenced by MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::MeshBasedCellPopulation().
bool MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mHasVariableRestLength [protected] |
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(), and MeshBasedCellPopulation< 2 >::serialize().
std::set< std::pair<Node<SPACE_DIM>*, Node<SPACE_DIM>* > > MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mNodePairs [protected] |
Node pairs for force calculations.
Definition at line 162 of file MeshBasedCellPopulation.hpp.
Referenced by MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::rGetNodePairs().
bool MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mOutputCellPopulationVolumes [protected] |
Whether to write the cell population volumes (in 3D) or areas (in 2D) to file.
Definition at line 153 of file MeshBasedCellPopulation.hpp.
Referenced by MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetOutputCellPopulationVolumes(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::OutputCellPopulationParameters(), MeshBasedCellPopulation< 2 >::serialize(), and MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::SetOutputCellPopulationVolumes().
bool MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mOutputVoronoiData [protected] |
Whether to write cell volume and surface area (in 3D) or area and perimeter (in 2D) information to file.
Definition at line 150 of file MeshBasedCellPopulation.hpp.
Referenced by MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetOutputVoronoiData(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::OutputCellPopulationParameters(), MeshBasedCellPopulation< 2 >::serialize(), and MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::SetOutputVoronoiData().
out_stream MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mpCellPopulationVolumesFile [protected] |
Results file for cell population volume (in 3D) or area (in 2D) data.
Definition at line 141 of file MeshBasedCellPopulation.hpp.
MutableMesh<ELEMENT_DIM, SPACE_DIM>* MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mpMutableMesh [protected] |
Static cast of the mesh from AbstractCellPopulation
Definition at line 121 of file MeshBasedCellPopulation.hpp.
Referenced by MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::MeshBasedCellPopulation().
out_stream MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mpVizElementsFile [protected] |
Results file for elements.
Definition at line 135 of file MeshBasedCellPopulation.hpp.
out_stream MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mpVoronoiFile [protected] |
Results file for Voronoi data.
Definition at line 138 of file MeshBasedCellPopulation.hpp.
VertexMesh<ELEMENT_DIM, SPACE_DIM>* MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mpVoronoiTessellation [protected] |
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 118 of file MeshBasedCellPopulation.hpp.
Referenced by MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::CreateVoronoiTessellation(), MeshBasedCellPopulation< 2 >::CreateVoronoiTessellation(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetSurfaceAreaOfVoronoiElement(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetVolumeOfVoronoiElement(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetVoronoiEdgeLength(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetVoronoiTessellation(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::MeshBasedCellPopulation(), and MeshBasedCellPopulation< 2 >::serialize().
std::map<std::pair<unsigned,unsigned>, double> MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mSpringRestLengths [protected] |
Keeps track of the rest lengths of springs if these are being used in the simulation.
Definition at line 132 of file MeshBasedCellPopulation.hpp.
Referenced by MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::CalculateRestLengths(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetRestLength(), and MeshBasedCellPopulation< 2 >::serialize().
bool MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mUseAreaBasedDampingConstant [protected] |
Whether to use a viscosity that is linear in the cell area, rather than constant.
Definition at line 144 of file MeshBasedCellPopulation.hpp.
Referenced by MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::OutputCellPopulationParameters(), and MeshBasedCellPopulation< 2 >::serialize().
bool MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mWriteVtkAsPoints [protected] |
Whether to write cells as points in VTK.
Definition at line 156 of file MeshBasedCellPopulation.hpp.
Referenced by MeshBasedCellPopulation< 2 >::serialize().
The documentation for this class was generated from the following files:
- cell_based/src/population/MeshBasedCellPopulation.hpp
- cell_based/src/population/MeshBasedCellPopulation.cpp
