AbstractCardiacCellFactory< ELEMENT_DIM, SPACE_DIM > Class Template Reference

#include <AbstractCardiacCellFactory.hpp>

Inherited by PlaneStimulusCellFactory< CELL, ELEMENT_DIM, SPACE_DIM >.

Collaboration diagram for AbstractCardiacCellFactory< ELEMENT_DIM, SPACE_DIM >:
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List of all members.

Public Member Functions

virtual AbstractCardiacCell * CreateCardiacCellForNode (unsigned nodeIndex)
virtual AbstractCardiacCell * CreateCardiacCellForTissueNode (unsigned nodeIndex)=0
virtual void FinaliseCellCreation (std::vector< AbstractCardiacCell * > *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 ()
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
FakeBathCell * mpFakeCell

Private Attributes

AbstractTetrahedralMesh
< ELEMENT_DIM, SPACE_DIM > * 		mpMesh
HeartGeometryInformation
< SPACE_DIM > * 		mpHeartGeometryInformation

Detailed Description

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>
class AbstractCardiacCellFactory< ELEMENT_DIM, SPACE_DIM >

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(unsigned), 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.

Definition at line 56 of file AbstractCardiacCellFactory.hpp.

Constructor & Destructor Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
AbstractCardiacCellFactory< ELEMENT_DIM, SPACE_DIM >::AbstractCardiacCellFactory ( boost::shared_ptr< AbstractIvpOdeSolver >  pSolver = boost::shared_ptr<AbstractIvpOdeSolver>(new EulerIvpOdeSolver)  )  [inline]

Default constructor.

Parameters:
pSolver the ODE solver to use to simulate this cell.

Definition at line 68 of file AbstractCardiacCellFactory.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
AbstractCardiacCellFactory< ELEMENT_DIM, SPACE_DIM >::~AbstractCardiacCellFactory (  )  [inline, virtual]

Destructor: free solver, zero stimulus and fake bath cell.

Definition at line 79 of file AbstractCardiacCellFactory.cpp.

References AbstractCardiacCellFactory< ELEMENT_DIM, SPACE_DIM >::mpFakeCell.

Member Function Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
AbstractCardiacCell * AbstractCardiacCellFactory< ELEMENT_DIM, SPACE_DIM >::CreateCardiacCellForNode ( unsigned  nodeIndex  )  [inline, virtual]

Create a cell object for the given node.

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).

Parameters:
nodeIndex Global node index.

Definition at line 33 of file AbstractCardiacCellFactory.cpp.

References HeartRegionCode::BATH, AbstractCardiacCellFactory< ELEMENT_DIM, SPACE_DIM >::CreateCardiacCellForTissueNode(), AbstractCardiacCellFactory< ELEMENT_DIM, SPACE_DIM >::mpFakeCell, and AbstractCardiacCellFactory< ELEMENT_DIM, SPACE_DIM >::mpMesh.

Referenced by AbstractCardiacPde< ELEMENT_DIM, SPACE_DIM >::AbstractCardiacPde().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>
virtual AbstractCardiacCell* AbstractCardiacCellFactory< ELEMENT_DIM, SPACE_DIM >::CreateCardiacCellForTissueNode ( unsigned  nodeIndex  )  [pure virtual]

Must be overridden by subclasses to return a cell object for the given node.

Parameters:
nodeIndex Global node index.

Implemented in RampedQuarterStimulusCellFactory< CELL, DIM >, BathCellFactory< DIM >, HeartConfigRelatedCellFactory< SPACE_DIM >, PlaneStimulusCellFactory< CELL, ELEMENT_DIM, SPACE_DIM >, and ZeroStimulusCellFactory< CELL, DIM >.

Referenced by AbstractCardiacCellFactory< ELEMENT_DIM, SPACE_DIM >::CreateCardiacCellForNode().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractCardiacCellFactory< ELEMENT_DIM, SPACE_DIM >::FillInCellularTransmuralAreas (  )  [inline, 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 55 of file AbstractCardiacCellFactory.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractCardiacCellFactory< ELEMENT_DIM, SPACE_DIM >::FinaliseCellCreation ( std::vector< AbstractCardiacCell * > *  pCellsDistributed,
unsigned  lo,
unsigned  hi 
) [inline, virtual]

May be overridden by subclasses to perform any necessary work after all cells have been created.

Parameters:
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 47 of file AbstractCardiacCellFactory.cpp.

Referenced by AbstractCardiacPde< ELEMENT_DIM, SPACE_DIM >::AbstractCardiacPde().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
HeartGeometryInformation< SPACE_DIM > * AbstractCardiacCellFactory< ELEMENT_DIM, SPACE_DIM >::GetHeartGeometryInformation (  )  [inline]
Returns:
the HeartGeometryInformation object

Definition at line 107 of file AbstractCardiacCellFactory.cpp.

References AbstractCardiacCellFactory< ELEMENT_DIM, SPACE_DIM >::mpHeartGeometryInformation.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > * AbstractCardiacCellFactory< ELEMENT_DIM, SPACE_DIM >::GetMesh (  )  [inline]
Returns:
the mesh used to create the cells.

Definition at line 91 of file AbstractCardiacCellFactory.cpp.

References AbstractCardiacCellFactory< ELEMENT_DIM, SPACE_DIM >::mpMesh.

Referenced by AbstractCardiacPde< ELEMENT_DIM, SPACE_DIM >::AbstractCardiacPde(), and PlaneStimulusCellFactory< CELL, ELEMENT_DIM, SPACE_DIM >::CreateCardiacCellForTissueNode().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
unsigned AbstractCardiacCellFactory< ELEMENT_DIM, SPACE_DIM >::GetNumberOfCells (  )  [inline, virtual]
Returns:
The number of cells

Definition at line 61 of file AbstractCardiacCellFactory.cpp.

References AbstractCardiacCellFactory< ELEMENT_DIM, SPACE_DIM >::mpMesh.

Referenced by AbstractCardiacPde< ELEMENT_DIM, SPACE_DIM >::AbstractCardiacPde(), and BidomainPde< SPACE_DIM >::BidomainPde().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractCardiacCellFactory< ELEMENT_DIM, SPACE_DIM >::SetHeartGeometryInformation ( HeartGeometryInformation< SPACE_DIM > *  pHeartGeometryInformation  )  [inline]

Set the HeartGeometryInformation object

Parameters:
pHeartGeometryInformation the HeartGeometryInformation object that is to be set

Definition at line 101 of file AbstractCardiacCellFactory.cpp.

References AbstractCardiacCellFactory< ELEMENT_DIM, SPACE_DIM >::mpHeartGeometryInformation.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractCardiacCellFactory< ELEMENT_DIM, SPACE_DIM >::SetMesh ( AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *  pMesh  )  [inline]
Parameters:
pMesh the mesh for which to create cardiac cells.

Definition at line 85 of file AbstractCardiacCellFactory.cpp.

References AbstractCardiacCellFactory< ELEMENT_DIM, SPACE_DIM >::mpMesh.

Member Data Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>
FakeBathCell* AbstractCardiacCellFactory< ELEMENT_DIM, SPACE_DIM >::mpFakeCell [protected]

A fake cell object to use at bath nodes.

We could use a base class pointer here, but that leads to confusing Boost serialization errors (unregistered class) as the FakeBathCell export line doesn't get seen by the archives.

Definition at line 82 of file AbstractCardiacCellFactory.hpp.

Referenced by AbstractCardiacCellFactory< ELEMENT_DIM, SPACE_DIM >::CreateCardiacCellForNode(), and AbstractCardiacCellFactory< ELEMENT_DIM, SPACE_DIM >::~AbstractCardiacCellFactory().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>
HeartGeometryInformation<SPACE_DIM>* AbstractCardiacCellFactory< ELEMENT_DIM, SPACE_DIM >::mpHeartGeometryInformation [private]

A pointer to an HeartGeometryInformation information object Can be accessed via get and set methods in this class.

Definition at line 68 of file AbstractCardiacCellFactory.hpp.

Referenced by AbstractCardiacCellFactory< ELEMENT_DIM, SPACE_DIM >::GetHeartGeometryInformation(), and AbstractCardiacCellFactory< ELEMENT_DIM, SPACE_DIM >::SetHeartGeometryInformation().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>
AbstractTetrahedralMesh<ELEMENT_DIM,SPACE_DIM>* AbstractCardiacCellFactory< ELEMENT_DIM, SPACE_DIM >::mpMesh [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 62 of file AbstractCardiacCellFactory.hpp.

Referenced by AbstractCardiacCellFactory< ELEMENT_DIM, SPACE_DIM >::CreateCardiacCellForNode(), AbstractCardiacCellFactory< ELEMENT_DIM, SPACE_DIM >::GetMesh(), AbstractCardiacCellFactory< ELEMENT_DIM, SPACE_DIM >::GetNumberOfCells(), and AbstractCardiacCellFactory< ELEMENT_DIM, SPACE_DIM >::SetMesh().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>
boost::shared_ptr<AbstractIvpOdeSolver> AbstractCardiacCellFactory< ELEMENT_DIM, SPACE_DIM >::mpSolver [protected]

The solver to give each of the cells

Definition at line 74 of file AbstractCardiacCellFactory.hpp.

Referenced by PlaneStimulusCellFactory< CELL, ELEMENT_DIM, SPACE_DIM >::CreateCardiacCellForTissueNode().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>
boost::shared_ptr<ZeroStimulus> AbstractCardiacCellFactory< ELEMENT_DIM, SPACE_DIM >::mpZeroStimulus [protected]

For use at un-stimulated cells.

Definition at line 72 of file AbstractCardiacCellFactory.hpp.

Referenced by PlaneStimulusCellFactory< CELL, ELEMENT_DIM, SPACE_DIM >::CreateCardiacCellForTissueNode().

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