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Chaste Commit::333233612e3dcc941d260418acd7b5ccdc30390e
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#include <AbstractCardiacCellFactory.hpp>
Public Member Functions | |
virtual AbstractCardiacCellInterface * | CreateCardiacCellForNode (Node< SPACE_DIM > *pNode) |
virtual AbstractCardiacCellInterface * | CreateCardiacCellForTissueNode (Node< SPACE_DIM > *pNode)=0 |
virtual void | FinaliseCellCreation (std::vector< AbstractCardiacCellInterface * > *pCellsDistributed, unsigned lo, unsigned hi) |
virtual void | FillInCellularTransmuralAreas () |
virtual unsigned | GetNumberOfCells () |
AbstractCardiacCellFactory (boost::shared_ptr< AbstractIvpOdeSolver > pSolver=boost::shared_ptr< AbstractIvpOdeSolver >(new EulerIvpOdeSolver)) | |
virtual | ~AbstractCardiacCellFactory () |
virtual void | SetMesh (AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *pMesh) |
AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > * | GetMesh () |
void | SetHeartGeometryInformation (HeartGeometryInformation< SPACE_DIM > *pHeartGeometryInformation) |
HeartGeometryInformation< SPACE_DIM > * | GetHeartGeometryInformation () |
Protected Attributes | |
boost::shared_ptr< ZeroStimulus > | mpZeroStimulus |
boost::shared_ptr< AbstractIvpOdeSolver > | mpSolver |
Private Attributes | |
AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > * | mpMesh |
HeartGeometryInformation< SPACE_DIM > * | mpHeartGeometryInformation |
A factory to ease creating cardiac cell objects for use in a mono/bidomain simulation.
The user should implement their own concrete class, in particular implementing CreateCardiacCellForTissueNode(Node*), which should return the cell corresponding to a given node. The user should also implement GetNumberOfCells() if this isn't equal to the number of nodes. FinaliseCellCreation() can be used to (eg) add stimuli to certain cells after they have been created.
This class saves the user having to create cells in parallel, that work is done by the pde instead.
ELEMENT_DIM | Dimension of the elements. |
SPACE_DIM | Dimension of the space. If not specified, it defaults to ELEMENT_DIM. |
Definition at line 70 of file AbstractCardiacCellFactory.hpp.
AbstractCardiacCellFactory< ELEMENT_DIM, SPACE_DIM >::AbstractCardiacCellFactory | ( | boost::shared_ptr< AbstractIvpOdeSolver > | pSolver = boost::shared_ptr<AbstractIvpOdeSolver>(new EulerIvpOdeSolver) | ) |
Default constructor.
pSolver | the ODE solver to use to simulate this cell. |
Definition at line 93 of file AbstractCardiacCellFactory.cpp.
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virtual |
Destructor: free solver, zero stimulus and fake bath cell.
Definition at line 103 of file AbstractCardiacCellFactory.cpp.
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virtual |
The default implementation checks whether the node is in the bath (in which case a pointer to a (unique) fake cell is returned) and if not, calls CreateCardiacCellForTissueNode (which must be defined by subclasses).
pNode | Pointer to node object. |
Definition at line 42 of file AbstractCardiacCellFactory.cpp.
References HeartConfig::GetPdeTimeStep(), Node< SPACE_DIM >::GetRegion(), HeartConfig::Instance(), and HeartRegionCode::IsRegionBath().
Referenced by AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::AbstractCardiacTissue(), and ExtendedBidomainTissue< SPACE_DIM >::ExtendedBidomainTissue().
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pure virtual |
Must be overridden by subclasses to return a cell object for the given node.
pNode | Pointer to node object. |
Implemented in HeartConfigRelatedCellFactory< SPACE_DIM >, PlaneStimulusCellFactory< CELL, ELEMENT_DIM, SPACE_DIM >, and PlaneStimulusCellFactory< CELL, ELEMENT_DIM, ELEMENT_DIM >.
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virtual |
Method that fills in the vector of heterogeneity areas with the NodesLists that correspond to a given layer (implemented in subclasses)
Reimplemented in HeartConfigRelatedCellFactory< SPACE_DIM >, and HeartConfigRelatedCellFactory< SPACE_DIM >.
Definition at line 78 of file AbstractCardiacCellFactory.cpp.
References EXCEPTION.
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virtual |
May be overridden by subclasses to perform any necessary work after all cells have been created.
pCellsDistributed | Pointer to a vector of cardiac cell pointers. |
lo | Lowest index owned by this process. |
hi | Highest index owned by this process. |
Definition at line 70 of file AbstractCardiacCellFactory.cpp.
Referenced by AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::AbstractCardiacTissue(), and ExtendedBidomainTissue< SPACE_DIM >::ExtendedBidomainTissue().
HeartGeometryInformation< SPACE_DIM > * AbstractCardiacCellFactory< ELEMENT_DIM, SPACE_DIM >::GetHeartGeometryInformation | ( | ) |
Definition at line 130 of file AbstractCardiacCellFactory.cpp.
References EXCEPTION.
AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > * AbstractCardiacCellFactory< ELEMENT_DIM, SPACE_DIM >::GetMesh | ( | ) |
Definition at line 114 of file AbstractCardiacCellFactory.cpp.
Referenced by AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::AbstractCardiacTissue(), and ExtendedBidomainTissue< SPACE_DIM >::ExtendedBidomainTissue().
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virtual |
Definition at line 86 of file AbstractCardiacCellFactory.cpp.
Referenced by AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::AbstractCardiacTissue(), and ExtendedBidomainTissue< SPACE_DIM >::ExtendedBidomainTissue().
void AbstractCardiacCellFactory< ELEMENT_DIM, SPACE_DIM >::SetHeartGeometryInformation | ( | HeartGeometryInformation< SPACE_DIM > * | pHeartGeometryInformation | ) |
Set the HeartGeometryInformation object
pHeartGeometryInformation | the HeartGeometryInformation object that is to be set |
Definition at line 124 of file AbstractCardiacCellFactory.cpp.
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virtual |
pMesh | the mesh for which to create cardiac cells. |
Reimplemented in AbstractPurkinjeCellFactory< ELEMENT_DIM, SPACE_DIM >.
Definition at line 108 of file AbstractCardiacCellFactory.cpp.
Referenced by CardiacSimulation::CreateAndRun(), and AbstractPurkinjeCellFactory< ELEMENT_DIM, SPACE_DIM >::SetMesh().
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private |
A pointer to an HeartGeometryInformation information object Can be accessed via get and set methods in this class.
Definition at line 82 of file AbstractCardiacCellFactory.hpp.
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private |
The mesh is automatically set in MonodomainProblem and BidomainProblem. This member variable should be accessed through GetMesh(), which will check if it has been set before and throw an exception otherwise.
Definition at line 76 of file AbstractCardiacCellFactory.hpp.
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protected |
The solver to give each of the cells
Definition at line 88 of file AbstractCardiacCellFactory.hpp.
Referenced by PlaneStimulusCellFactory< CELL, ELEMENT_DIM, SPACE_DIM >::CreateCardiacCellForTissueNode().
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protected |
For use at un-stimulated cells.
Definition at line 86 of file AbstractCardiacCellFactory.hpp.
Referenced by PlaneStimulusCellFactory< CELL, ELEMENT_DIM, SPACE_DIM >::CreateCardiacCellForTissueNode().