Chaste Commit::baa90ac2819b962188b7562f2326be23c47859a7
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#include <VolumeTrackingModifier.hpp>
Public Member Functions | |
VolumeTrackingModifier () | |
virtual | ~VolumeTrackingModifier () |
virtual void | UpdateAtEndOfTimeStep (AbstractCellPopulation< DIM, DIM > &rCellPopulation) |
virtual void | SetupSolve (AbstractCellPopulation< DIM, DIM > &rCellPopulation, std::string outputDirectory) |
void | UpdateCellData (AbstractCellPopulation< DIM, DIM > &rCellPopulation) |
void | OutputSimulationModifierParameters (out_stream &rParamsFile) |
Public Member Functions inherited from AbstractCellBasedSimulationModifier< DIM, DIM > | |
AbstractCellBasedSimulationModifier () | |
virtual | ~AbstractCellBasedSimulationModifier () |
virtual void | UpdateAtEndOfTimeStep (AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > &rCellPopulation)=0 |
virtual void | UpdateAtEndOfOutputTimeStep (AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > &rCellPopulation) |
virtual void | SetupSolve (AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > &rCellPopulation, std::string outputDirectory)=0 |
virtual void | UpdateAtEndOfSolve (AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > &rCellPopulation) |
void | OutputSimulationModifierInfo (out_stream &rParamsFile) |
Public Member Functions inherited from Identifiable | |
virtual | ~Identifiable () |
std::string | GetIdentifier () const |
Private Member Functions | |
template<class Archive > | |
void | serialize (Archive &archive, const unsigned int version) |
Friends | |
class | boost::serialization::access |
A modifier class which at each simulation time step calculates the volume of each cell and stores it in in the CellData property as "volume". To be used in conjunction with contact inhibition cell cycle models.
Definition at line 50 of file VolumeTrackingModifier.hpp.
VolumeTrackingModifier< DIM >::VolumeTrackingModifier | ( | ) |
Default constructor.
Definition at line 40 of file VolumeTrackingModifier.cpp.
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virtual |
Destructor.
Definition at line 46 of file VolumeTrackingModifier.cpp.
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virtual |
Overridden OutputSimulationModifierParameters() method. Output any simulation modifier parameters to file.
rParamsFile | the file stream to which the parameters are output |
Implements AbstractCellBasedSimulationModifier< DIM, DIM >.
Definition at line 100 of file VolumeTrackingModifier.cpp.
References AbstractCellBasedSimulationModifier< ELEMENT_DIM, SPACE_DIM >::OutputSimulationModifierParameters().
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inlineprivate |
Boost Serialization method for archiving/checkpointing. Archives the object and its member variables.
archive | The boost archive. |
version | The current version of this class. |
Definition at line 62 of file VolumeTrackingModifier.hpp.
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virtual |
Overridden SetupSolve() method.
Specify what to do in the simulation before the start of the time loop.
rCellPopulation | reference to the cell population |
outputDirectory | the output directory, relative to where Chaste output is stored |
Definition at line 57 of file VolumeTrackingModifier.cpp.
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virtual |
Overridden UpdateAtEndOfTimeStep() method.
Specify what to do in the simulation at the end of each time step.
rCellPopulation | reference to the cell population |
Definition at line 51 of file VolumeTrackingModifier.cpp.
void VolumeTrackingModifier< DIM >::UpdateCellData | ( | AbstractCellPopulation< DIM, DIM > & | rCellPopulation | ) |
Helper method to compute the volume of each cell in the population and store these in the CellData.
rCellPopulation | reference to the cell population |
This hack is needed because in the case of a MeshBasedCellPopulation in which multiple cell divisions have occurred over one time step, the Voronoi tessellation (while existing) is out-of-date. Thus, if we did not regenerate the Voronoi tessellation here, an assertion may trip as we try to access a Voronoi element whose index exceeds the number of elements in the out-of-date tessellation.
Definition at line 67 of file VolumeTrackingModifier.cpp.
References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::Begin(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::CreateVoronoiTessellation(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::End(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetVolumeOfCell(), and AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::Update().
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friend |
Needed for serialization.
Definition at line 53 of file VolumeTrackingModifier.hpp.