AbstractOnLatticeCellPopulation< DIM > Class Template Reference
#include <AbstractOnLatticeCellPopulation.hpp>
Inherits AbstractCellPopulation< DIM >.
Inherited by CaBasedCellPopulation< DIM >, and PottsBasedCellPopulation< DIM >.
Public Member Functions | |
| AbstractOnLatticeCellPopulation (std::vector< CellPtr > &rCells, const std::vector< unsigned > locationIndices=std::vector< unsigned >(), bool deleteMesh=false) | |
| virtual | ~AbstractOnLatticeCellPopulation () |
| virtual void | UpdateCellLocations (double dt)=0 |
| bool | GetUpdateNodesInRandomOrder () |
| void | SetUpdateNodesInRandomOrder (bool updateNodesInRandomOrder) |
| void | SetIterateRandomlyOverUpdateRuleCollection (bool iterateRandomly) |
| bool | GetIterateRandomlyOverUpdateRuleCollection () |
| void | SetNode (unsigned index, ChastePoint< DIM > &rNewLocation) |
| virtual void | OutputCellPopulationParameters (out_stream &rParamsFile) |
Protected Member Functions | |
| AbstractOnLatticeCellPopulation () | |
Protected Attributes | |
| bool | mDeleteMesh |
| bool | mUpdateNodesInRandomOrder |
| bool | mIterateRandomlyOverUpdateRuleCollection |
Private Member Functions | |
| template<class Archive > | |
| void | serialize (Archive &archive, const unsigned int version) |
Friends | |
| class | boost::serialization::access |
Detailed Description
template<unsigned DIM>
class AbstractOnLatticeCellPopulation< DIM >
An abstract class for on-lattice cell populations.
Definition at line 41 of file AbstractOnLatticeCellPopulation.hpp.
Constructor & Destructor Documentation
| AbstractOnLatticeCellPopulation< DIM >::AbstractOnLatticeCellPopulation | ( | ) | [inline, protected] |
Constructor for use by archiving only.
Definition at line 43 of file AbstractOnLatticeCellPopulation.cpp.
| AbstractOnLatticeCellPopulation< DIM >::AbstractOnLatticeCellPopulation | ( | std::vector< CellPtr > & | rCells, | |
| const std::vector< unsigned > | locationIndices = std::vector<unsigned>(), |
|||
| bool | deleteMesh = false | |||
| ) | [inline] |
Default constructor.
- Parameters:
-
rCells a vector of cells 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 (defaults to false)
Definition at line 32 of file AbstractOnLatticeCellPopulation.cpp.
| AbstractOnLatticeCellPopulation< DIM >::~AbstractOnLatticeCellPopulation | ( | ) | [inline, virtual] |
Destructor.
Definition at line 52 of file AbstractOnLatticeCellPopulation.cpp.
Member Function Documentation
| bool AbstractOnLatticeCellPopulation< DIM >::GetIterateRandomlyOverUpdateRuleCollection | ( | ) | [inline] |
- Returns:
- mIterateRandomlyOverUpdateRuleCollection.
Definition at line 75 of file AbstractOnLatticeCellPopulation.cpp.
References AbstractOnLatticeCellPopulation< DIM >::mIterateRandomlyOverUpdateRuleCollection.
| bool AbstractOnLatticeCellPopulation< DIM >::GetUpdateNodesInRandomOrder | ( | ) | [inline] |
Get whether we update nodes in a random order.
- Returns:
- mUpdateNodesInRandomOrder
Definition at line 57 of file AbstractOnLatticeCellPopulation.cpp.
References AbstractOnLatticeCellPopulation< DIM >::mUpdateNodesInRandomOrder.
| void AbstractOnLatticeCellPopulation< DIM >::OutputCellPopulationParameters | ( | out_stream & | rParamsFile | ) | [inline, virtual] |
Outputs CellPopulation parameters to file
- Parameters:
-
rParamsFile the file stream to which the parameters are output
Implements AbstractCellPopulation< DIM >.
Reimplemented in CaBasedCellPopulation< DIM >, and PottsBasedCellPopulation< DIM >.
Definition at line 87 of file AbstractOnLatticeCellPopulation.cpp.
References AbstractOnLatticeCellPopulation< DIM >::mIterateRandomlyOverUpdateRuleCollection, and AbstractOnLatticeCellPopulation< DIM >::mUpdateNodesInRandomOrder.
| void AbstractOnLatticeCellPopulation< DIM >::serialize | ( | Archive & | archive, | |
| const unsigned int | version | |||
| ) | [inline, private] |
Serialize the object and its member variables.
- Parameters:
-
archive the archive version the current version of this class
Reimplemented from AbstractCellPopulation< DIM >.
Reimplemented in CaBasedCellPopulation< DIM >, and PottsBasedCellPopulation< DIM >.
Definition at line 54 of file AbstractOnLatticeCellPopulation.hpp.
References AbstractOnLatticeCellPopulation< DIM >::mIterateRandomlyOverUpdateRuleCollection, and AbstractOnLatticeCellPopulation< DIM >::mUpdateNodesInRandomOrder.
| void AbstractOnLatticeCellPopulation< DIM >::SetIterateRandomlyOverUpdateRuleCollection | ( | bool | iterateRandomly | ) | [inline] |
Set mIterateRandomlyOverUpdateRuleCollection.
- Parameters:
-
iterateRandomly whether to iterate randomly over mUpdateRuleCollection
Definition at line 69 of file AbstractOnLatticeCellPopulation.cpp.
References AbstractOnLatticeCellPopulation< DIM >::mIterateRandomlyOverUpdateRuleCollection.
| void AbstractOnLatticeCellPopulation< DIM >::SetNode | ( | unsigned | index, | |
| ChastePoint< DIM > & | rNewLocation | |||
| ) | [inline, virtual] |
Overridden SetNode() method.
This method throws an exception if called on a subclass of AbstractOnLatticeCellPopulation, since in such classes the lattice is assumed to be fixed.
- Parameters:
-
index the index of the node to be moved rNewLocation the new target location of the node
Implements AbstractCellPopulation< DIM >.
Definition at line 81 of file AbstractOnLatticeCellPopulation.cpp.
References EXCEPTION.
| void AbstractOnLatticeCellPopulation< DIM >::SetUpdateNodesInRandomOrder | ( | bool | updateNodesInRandomOrder | ) | [inline] |
Get whether we update nodes in a random order.
- Parameters:
-
updateNodesInRandomOrder Whether to update nodes in a random order.
Definition at line 63 of file AbstractOnLatticeCellPopulation.cpp.
References AbstractOnLatticeCellPopulation< DIM >::mUpdateNodesInRandomOrder.
| virtual void AbstractOnLatticeCellPopulation< DIM >::UpdateCellLocations | ( | double | dt | ) | [pure virtual] |
Update cell locations over the course of a time step of specified length.
As this method is pure virtual, it must be overridden in subclasses.
- Parameters:
-
dt time step
Implemented in CaBasedCellPopulation< DIM >, and PottsBasedCellPopulation< DIM >.
Friends And Related Function Documentation
friend class boost::serialization::access [friend] |
Needed for serialization.
Reimplemented from AbstractCellPopulation< DIM >.
Reimplemented in CaBasedCellPopulation< DIM >, and PottsBasedCellPopulation< DIM >.
Definition at line 46 of file AbstractOnLatticeCellPopulation.hpp.
Member Data Documentation
bool AbstractOnLatticeCellPopulation< DIM >::mDeleteMesh [protected] |
Whether to delete the mesh when we are destroyed. Needed if this cell population has been de-serialized.
Definition at line 67 of file AbstractOnLatticeCellPopulation.hpp.
Referenced by CaBasedCellPopulation< DIM >::~CaBasedCellPopulation(), and PottsBasedCellPopulation< DIM >::~PottsBasedCellPopulation().
bool AbstractOnLatticeCellPopulation< DIM >::mIterateRandomlyOverUpdateRuleCollection [protected] |
Whether to iterate randomly over mUpdateRuleCollection when updating cell locations. Initialized to false in the constructor.
Definition at line 79 of file AbstractOnLatticeCellPopulation.hpp.
Referenced by AbstractOnLatticeCellPopulation< DIM >::GetIterateRandomlyOverUpdateRuleCollection(), AbstractOnLatticeCellPopulation< DIM >::OutputCellPopulationParameters(), AbstractOnLatticeCellPopulation< DIM >::serialize(), AbstractOnLatticeCellPopulation< DIM >::SetIterateRandomlyOverUpdateRuleCollection(), PottsBasedCellPopulation< DIM >::UpdateCellLocations(), and CaBasedCellPopulation< DIM >::UpdateCellLocations().
bool AbstractOnLatticeCellPopulation< DIM >::mUpdateNodesInRandomOrder [protected] |
Whether to update nodes in random order. Initialized to true in the constructor.
Definition at line 73 of file AbstractOnLatticeCellPopulation.hpp.
Referenced by AbstractOnLatticeCellPopulation< DIM >::GetUpdateNodesInRandomOrder(), AbstractOnLatticeCellPopulation< DIM >::OutputCellPopulationParameters(), AbstractOnLatticeCellPopulation< DIM >::serialize(), AbstractOnLatticeCellPopulation< DIM >::SetUpdateNodesInRandomOrder(), PottsBasedCellPopulation< DIM >::UpdateCellLocations(), and CaBasedCellPopulation< DIM >::UpdateCellLocations().
The documentation for this class was generated from the following files:
- cell_based/src/population/AbstractOnLatticeCellPopulation.hpp
- cell_based/src/population/AbstractOnLatticeCellPopulation.cpp
