Chaste Commit::baa90ac2819b962188b7562f2326be23c47859a7
Public Member Functions | Private Member Functions | Friends | List of all members
CellDeltaNotchWriter< ELEMENT_DIM, SPACE_DIM > Class Template Reference

#include <CellDeltaNotchWriter.hpp>

+ Inheritance diagram for CellDeltaNotchWriter< ELEMENT_DIM, SPACE_DIM >:
+ Collaboration diagram for CellDeltaNotchWriter< ELEMENT_DIM, SPACE_DIM >:

Public Member Functions

 CellDeltaNotchWriter ()
 
double GetCellDataForVtkOutput (CellPtr pCell, AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > *pCellPopulation)
 
virtual void VisitCell (CellPtr pCell, AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > *pCellPopulation)
 
- Public Member Functions inherited from AbstractCellWriter< ELEMENT_DIM, SPACE_DIM >
 AbstractCellWriter (const std::string &rFileName)
 
virtual c_vector< double, SPACE_DIM > GetVectorCellDataForVtkOutput (CellPtr pCell, AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > *pCellPopulation)
 
bool GetOutputScalarData ()
 
bool GetOutputVectorData ()
 
void SetVtkCellDataName (std::string vtkCellDataName)
 
void SetVtkVectorCellDataName (std::string vtkCellDataName)
 
std::string GetVtkCellDataName ()
 
std::string GetVtkVectorCellDataName ()
 
- Public Member Functions inherited from AbstractCellBasedWriter< ELEMENT_DIM, SPACE_DIM >
 AbstractCellBasedWriter (const std::string &rFileName)
 
virtual ~AbstractCellBasedWriter ()
 
void CloseFile ()
 
virtual void OpenOutputFile (OutputFileHandler &rOutputFileHandler)
 
void OpenOutputFileForAppend (OutputFileHandler &rOutputFileHandler)
 
virtual void WriteTimeStamp ()
 
virtual void WriteNewline ()
 
void SetFileName (std::string fileName)
 
std::string GetFileName ()
 
- 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
 

Additional Inherited Members

- Protected Attributes inherited from AbstractCellWriter< ELEMENT_DIM, SPACE_DIM >
bool mOutputScalarData
 
bool mOutputVectorData
 
std::string mVtkCellDataName
 
std::string mVtkVectorCellDataName
 
- Protected Attributes inherited from AbstractCellBasedWriter< ELEMENT_DIM, SPACE_DIM >
std::string mFileName
 
out_stream mpOutStream
 

Detailed Description

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
class CellDeltaNotchWriter< ELEMENT_DIM, SPACE_DIM >

A class written using the visitor pattern for writing to file, for each cell, the level of delta, notch and mean level of delta among neighbouring cells.

The output file is called celldeltanotch.dat by default. If VTK is switched on, then the writer also specifies the VTK output for each cell, which is stored in the VTK cell data "Cell delta" by default.

Note: if you use a DeltaNotchSrnModel then the delta and notch levels are stored in CellData, and thus (if VTK is switched on) will be output as VTK cell data already.

Definition at line 56 of file CellDeltaNotchWriter.hpp.

Constructor & Destructor Documentation

◆ CellDeltaNotchWriter()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
CellDeltaNotchWriter< ELEMENT_DIM, SPACE_DIM >::CellDeltaNotchWriter ( )

Default constructor.

Definition at line 40 of file CellDeltaNotchWriter.cpp.

References AbstractCellWriter< ELEMENT_DIM, SPACE_DIM >::mVtkCellDataName.

Member Function Documentation

◆ GetCellDataForVtkOutput()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
double CellDeltaNotchWriter< ELEMENT_DIM, SPACE_DIM >::GetCellDataForVtkOutput ( CellPtr  pCell,
AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > *  pCellPopulation 
)
virtual

Overridden GetCellDataForVtkOutput() method.

Get a double associated with a cell. This method reduces duplication of code between the methods VisitCell() and AddVtkData().

Parameters
pCella cell
pCellPopulationa pointer to the cell population owning the cell
Returns
data associated with the cell

Reimplemented from AbstractCellWriter< ELEMENT_DIM, SPACE_DIM >.

Definition at line 47 of file CellDeltaNotchWriter.cpp.

◆ serialize()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
template<class Archive >
void CellDeltaNotchWriter< ELEMENT_DIM, SPACE_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 68 of file CellDeltaNotchWriter.hpp.

◆ VisitCell()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void CellDeltaNotchWriter< ELEMENT_DIM, SPACE_DIM >::VisitCell ( CellPtr  pCell,
AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > *  pCellPopulation 
)
virtual

Overridden VisitCell() method.

Visit a cell and write its delta and notch data.

Outputs a line of space-separated values of the form: ...[location index] [cell id] [x-pos] [y-pos] [z-pos] [delta] [notch] [mean neighbouring delta]... with [y-pos] and [z-pos] included for 2 and 3 dimensional simulations, respectively.

This is appended to the output written by AbstractCellBasedWriter, which is a single value [present simulation time], followed by a tab.

Parameters
pCella cell
pCellPopulationa pointer to the cell population owning the cell

Implements AbstractCellWriter< ELEMENT_DIM, SPACE_DIM >.

Definition at line 54 of file CellDeltaNotchWriter.cpp.

References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetLocationIndexUsingCell(), and AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetLocationOfCellCentre().

Friends And Related Symbol Documentation

◆ boost::serialization::access

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
friend class boost::serialization::access
friend

Needed for serialization.

Definition at line 60 of file CellDeltaNotchWriter.hpp.

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