HoneycombMeshGenerator Class Reference

#include <HoneycombMeshGenerator.hpp>

Inheritance diagram for HoneycombMeshGenerator:

Collaboration diagram for HoneycombMeshGenerator:

Public Member Functions
	HoneycombMeshGenerator (unsigned numNodesAlongWidth, unsigned numNodesAlongLength, unsigned ghosts=0, double scaleFactor=1.0)
	HoneycombMeshGenerator ()
virtual	~HoneycombMeshGenerator ()=default
virtual boost::shared_ptr< MutableMesh< 2, 2 > >	GetMesh ()
std::vector< unsigned >	GetCellLocationIndices ()
boost::shared_ptr< MutableMesh< 2, 2 > >	GetCircularMesh (double radius)
double	GetDomainDepth ()
double	GetDomainWidth ()

Protected Attributes
boost::shared_ptr< MutableMesh< 2, 2 > >	mpMesh
std::set< unsigned >	mGhostNodeIndices
std::string	mMeshFilename
double	mDomainWidth
double	mDomainDepth
double	mBottom
double	mTop
unsigned	mNumCellWidth
unsigned	mNumCellLength

Detailed Description

Honeycomb mesh generator that creates a 2D honeycomb mesh (with equal distance between nodes) for use in cell-centre simulations.

NOTE: the user should delete the mesh after use to manage memory.

Definition at line 51 of file HoneycombMeshGenerator.hpp.

Constructor & Destructor Documentation

HoneycombMeshGenerator() [1/2]

HoneycombMeshGenerator::HoneycombMeshGenerator	(	unsigned	numNodesAlongWidth,
		unsigned	numNodesAlongLength,
		unsigned	ghosts = 0,
		double	scaleFactor = 1.0
	)

Default constructor.

Parameters

numNodesAlongWidth	The number of cells you want alopng the bottom of the domain
numNodesAlongLength	The number of cells you want sides of the domain
ghosts	The thickness of ghost nodes to put around the edge (defaults to 0)
scaleFactor	The scale factor for the width (circumference) of the cells (defaults to 1.0)

Definition at line 48 of file HoneycombMeshGenerator.cpp.

References OutputFileHandler::FindFile(), OutputFileHandler::GetOutputDirectoryFullPath(), PetscTools::IsSequential(), mBottom, mDomainDepth, mDomainWidth, mGhostNodeIndices, mMeshFilename, mNumCellLength, mNumCellWidth, mpMesh, mTop, OutputFileHandler::OpenOutputFile(), and FileFinder::Remove().

HoneycombMeshGenerator() [2/2]

HoneycombMeshGenerator::HoneycombMeshGenerator ( )

inline

Null constructor for derived classes to call.

Definition at line 97 of file HoneycombMeshGenerator.hpp.

~HoneycombMeshGenerator()

virtual HoneycombMeshGenerator::~HoneycombMeshGenerator ( )

virtualdefault

Empty destructor.

Member Function Documentation

GetCellLocationIndices()

std::vector< unsigned > HoneycombMeshGenerator::GetCellLocationIndices

(

)

Returns the indices of the nodes in the mesh which correspond to real cells. This information is needed when constructing a MeshBasedCellPopulationWithGhostNodes.

Returns

indices of nodes

Definition at line 236 of file HoneycombMeshGenerator.cpp.

References mGhostNodeIndices, and mpMesh.

GetCircularMesh()

boost::shared_ptr< MutableMesh< 2, 2 > > HoneycombMeshGenerator::GetCircularMesh

(

double

radius

)

Parameters

radius

the radius of the circular mesh

Returns

a honeycomb mesh constructed to be roughly circular.

Definition at line 250 of file HoneycombMeshGenerator.cpp.

References EXCEPTION, RandomNumberGenerator::Instance(), mGhostNodeIndices, mpMesh, and RandomNumberGenerator::ranf().

GetDomainDepth()

double HoneycombMeshGenerator::GetDomainDepth

(

)

Returns

mDomainDepth

Definition at line 294 of file HoneycombMeshGenerator.cpp.

References mDomainDepth.

GetDomainWidth()

double HoneycombMeshGenerator::GetDomainWidth

(

)

Returns

mDomainWidth

Definition at line 299 of file HoneycombMeshGenerator.cpp.

References mDomainWidth.

GetMesh()

boost::shared_ptr< MutableMesh< 2, 2 > > HoneycombMeshGenerator::GetMesh ( )

virtual

Returns

a 2D honeycomb mesh based on a 2D plane

Reimplemented in CylindricalHoneycombMeshGenerator, and ToroidalHoneycombMeshGenerator.

Definition at line 231 of file HoneycombMeshGenerator.cpp.

References mpMesh.

Member Data Documentation

mBottom

double HoneycombMeshGenerator::mBottom

protected

The y coordinate of the bottom row of cells (ghosts if requested)

Definition at line 71 of file HoneycombMeshGenerator.hpp.

Referenced by CylindricalHoneycombMeshGenerator::CylindricalHoneycombMeshGenerator(), and HoneycombMeshGenerator().

mDomainDepth

double HoneycombMeshGenerator::mDomainDepth

protected

The (y) depth of the domain to be constructed

Definition at line 68 of file HoneycombMeshGenerator.hpp.

Referenced by CylindricalHoneycombMeshGenerator::CylindricalHoneycombMeshGenerator(), HoneycombMeshGenerator(), ToroidalHoneycombMeshGenerator::ToroidalHoneycombMeshGenerator(), and GetDomainDepth().

mDomainWidth

double HoneycombMeshGenerator::mDomainWidth

protected

The (x) width of the domain to be constructed

Definition at line 65 of file HoneycombMeshGenerator.hpp.

Referenced by CylindricalHoneycombMeshGenerator::CylindricalHoneycombMeshGenerator(), HoneycombMeshGenerator(), ToroidalHoneycombMeshGenerator::ToroidalHoneycombMeshGenerator(), and GetDomainWidth().

mGhostNodeIndices

std::set<unsigned> HoneycombMeshGenerator::mGhostNodeIndices

protected

The indices of the nodes in this mesh which are 'ghost nodes'

Definition at line 59 of file HoneycombMeshGenerator.hpp.

Referenced by CylindricalHoneycombMeshGenerator::CylindricalHoneycombMeshGenerator(), HoneycombMeshGenerator(), GetCellLocationIndices(), and GetCircularMesh().

mMeshFilename

std::string HoneycombMeshGenerator::mMeshFilename

protected

The mesh is generated by writing out a series of nodes and reading them in from this file

Definition at line 62 of file HoneycombMeshGenerator.hpp.

Referenced by CylindricalHoneycombMeshGenerator::CylindricalHoneycombMeshGenerator(), HoneycombMeshGenerator(), and ToroidalHoneycombMeshGenerator::ToroidalHoneycombMeshGenerator().

mNumCellLength

unsigned HoneycombMeshGenerator::mNumCellLength

protected

The number of rows of cells to put up the y coordinate of the mesh

Definition at line 80 of file HoneycombMeshGenerator.hpp.

Referenced by CylindricalHoneycombMeshGenerator::CylindricalHoneycombMeshGenerator(), HoneycombMeshGenerator(), and ToroidalHoneycombMeshGenerator::ToroidalHoneycombMeshGenerator().

mNumCellWidth

unsigned HoneycombMeshGenerator::mNumCellWidth

protected

The number of columns of cells to put across the x coordinate of the mesh

Definition at line 77 of file HoneycombMeshGenerator.hpp.

Referenced by CylindricalHoneycombMeshGenerator::CylindricalHoneycombMeshGenerator(), HoneycombMeshGenerator(), and ToroidalHoneycombMeshGenerator::ToroidalHoneycombMeshGenerator().

mpMesh

boost::shared_ptr<MutableMesh<2,2> > HoneycombMeshGenerator::mpMesh

protected

A pointer to the mesh this class creates

Definition at line 56 of file HoneycombMeshGenerator.hpp.

Referenced by CylindricalHoneycombMeshGenerator::CylindricalHoneycombMeshGenerator(), HoneycombMeshGenerator(), ToroidalHoneycombMeshGenerator::ToroidalHoneycombMeshGenerator(), GetCellLocationIndices(), GetCircularMesh(), CylindricalHoneycombMeshGenerator::GetCylindricalMesh(), CylindricalHoneycombMeshGenerator::GetMesh(), GetMesh(), ToroidalHoneycombMeshGenerator::GetMesh(), and ToroidalHoneycombMeshGenerator::GetToroidalMesh().

mTop

double HoneycombMeshGenerator::mTop

protected

The y coordinate of the top row of cells (ghosts if requested)

Definition at line 74 of file HoneycombMeshGenerator.hpp.

Referenced by CylindricalHoneycombMeshGenerator::CylindricalHoneycombMeshGenerator(), and HoneycombMeshGenerator().

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

• mesh/src/mutable/HoneycombMeshGenerator.hpp
• mesh/src/mutable/HoneycombMeshGenerator.cpp