Chaste Commit::baa90ac2819b962188b7562f2326be23c47859a7
CryptSimulationBoundaryCondition< DIM > Class Template Reference

#include <CryptSimulationBoundaryCondition.hpp>

+ Inheritance diagram for CryptSimulationBoundaryCondition< DIM >:
+ Collaboration diagram for CryptSimulationBoundaryCondition< DIM >:

Public Member Functions

 CryptSimulationBoundaryCondition (AbstractCellPopulation< DIM > *pCellPopulation)
 
void ImposeBoundaryCondition (const std::map< Node< DIM > *, c_vector< double, DIM > > &rOldLocations)
 
bool VerifyBoundaryCondition ()
 
void SetUseJiggledBottomCells (bool useJiggledBottomCells)
 
bool GetUseJiggledBottomCells ()
 
void OutputCellPopulationBoundaryConditionParameters (out_stream &rParamsFile)
 
- Public Member Functions inherited from AbstractCellPopulationBoundaryCondition< DIM >
 AbstractCellPopulationBoundaryCondition (AbstractCellPopulation< ELEMENT_DIM, ELEMENT_DIM > *pCellPopulation)
 
virtual ~AbstractCellPopulationBoundaryCondition ()
 
virtual void ImposeBoundaryCondition (const std::map< Node< ELEMENT_DIM > *, c_vector< double, ELEMENT_DIM > > &rOldLocations)=0
 
const AbstractCellPopulation< ELEMENT_DIM, ELEMENT_DIM > * GetCellPopulation () const
 
void OutputCellPopulationBoundaryConditionInfo (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)
 

Private Attributes

bool mUseJiggledBottomCells
 

Friends

class boost::serialization::access
 

Additional Inherited Members

- Protected Attributes inherited from AbstractCellPopulationBoundaryCondition< DIM >
AbstractCellPopulation< ELEMENT_DIM, ELEMENT_DIM > * mpCellPopulation
 

Detailed Description

template<unsigned DIM>
class CryptSimulationBoundaryCondition< DIM >

A boundary condition class for use with CryptSimulation2d, which pins stem cells in the absence of a Wnt stimulus, and optionally prevents cells moving below the y=0 boundary via random jiggling.

Definition at line 51 of file CryptSimulationBoundaryCondition.hpp.

Constructor & Destructor Documentation

◆ CryptSimulationBoundaryCondition()

Constructor.

Parameters
pCellPopulationpointer to the cell population

Definition at line 43 of file CryptSimulationBoundaryCondition.cpp.

Member Function Documentation

◆ GetUseJiggledBottomCells()

template<unsigned DIM>
bool CryptSimulationBoundaryCondition< DIM >::GetUseJiggledBottomCells ( )

◆ ImposeBoundaryCondition()

template<unsigned DIM>
void CryptSimulationBoundaryCondition< DIM >::ImposeBoundaryCondition ( const std::map< Node< DIM > *, c_vector< double, DIM > > &  rOldLocations)

Overridden ImposeBoundaryCondition() method.

Apply the cell population boundary conditions.

Parameters
rOldLocationsthe node locations before any boundary conditions are applied

Definition at line 50 of file CryptSimulationBoundaryCondition.cpp.

References WntConcentration< DIM >::Destroy(), WntConcentration< DIM >::Instance(), RandomNumberGenerator::Instance(), WntConcentration< DIM >::IsWntSetUp(), RandomNumberGenerator::ranf(), Node< SPACE_DIM >::rGetLocation(), and Node< SPACE_DIM >::rGetModifiableLocation().

◆ OutputCellPopulationBoundaryConditionParameters()

template<unsigned DIM>
void CryptSimulationBoundaryCondition< DIM >::OutputCellPopulationBoundaryConditionParameters ( out_stream &  rParamsFile)
virtual

Overridden OutputCellPopulationBoundaryConditionParameters() method. Output cell population boundary condition parameters to file.

Parameters
rParamsFilethe file stream to which the parameters are output
Todo:
Can we abstract these XML out methods and do automatic indentation?

Implements AbstractCellPopulationBoundaryCondition< DIM >.

Definition at line 200 of file CryptSimulationBoundaryCondition.cpp.

References AbstractCellPopulationBoundaryCondition< ELEMENT_DIM, SPACE_DIM >::OutputCellPopulationBoundaryConditionParameters().

◆ serialize()

template<unsigned DIM>
template<class Archive >
void CryptSimulationBoundaryCondition< DIM >::serialize ( Archive &  archive,
const unsigned int  version 
)
inlineprivate

Serialize the object and its member variables.

Parameters
archivethe archive
versionthe current version of this class

Definition at line 70 of file CryptSimulationBoundaryCondition.hpp.

References CryptSimulationBoundaryCondition< DIM >::mUseJiggledBottomCells.

◆ SetUseJiggledBottomCells()

template<unsigned DIM>
void CryptSimulationBoundaryCondition< DIM >::SetUseJiggledBottomCells ( bool  useJiggledBottomCells)

Set method for mUseJiggledBottomCells

Parameters
useJiggledBottomCellswhether to jiggle the cells on the bottom surface

Definition at line 188 of file CryptSimulationBoundaryCondition.cpp.

◆ VerifyBoundaryCondition()

template<unsigned DIM>
bool CryptSimulationBoundaryCondition< DIM >::VerifyBoundaryCondition ( )
virtual

Overridden VerifyBoundaryCondition() method. Verify the boundary conditions have been applied. This is called after ImposeBoundaryCondition() to ensure the condition is still satisfied.

Returns
whether the boundary conditions are satisfied.

Implements AbstractCellPopulationBoundaryCondition< DIM >.

Definition at line 158 of file CryptSimulationBoundaryCondition.cpp.

References Node< SPACE_DIM >::rGetLocation().

Friends And Related Symbol Documentation

◆ boost::serialization::access

template<unsigned DIM>
friend class boost::serialization::access
friend

Needed for serialization.

Definition at line 62 of file CryptSimulationBoundaryCondition.hpp.

Member Data Documentation

◆ mUseJiggledBottomCells

template<unsigned DIM>
bool CryptSimulationBoundaryCondition< DIM >::mUseJiggledBottomCells
private

Whether to jiggle the cells on the bottom surface, initialised to false in the constructor.

Definition at line 59 of file CryptSimulationBoundaryCondition.hpp.

Referenced by CryptSimulationBoundaryCondition< DIM >::serialize().


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