MeshEntry Class Reference

#include <MeshEntry.h>

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List of all members.

Public Member Functions
	MeshEntry ()
	MeshEntry (const ChemCompt *parent)
double	getVolume (const Eref &e) const
unsigned int	getDimensions (const Eref &e) const
unsigned int	getMeshType (const Eref &e) const
vector< double >	getCoordinates (const Eref &e) const
vector< unsigned int >	getNeighbors (const Eref &e) const
vector< double >	getDiffusionArea (const Eref &e) const
vector< double >	getDiffusionScaling (const Eref &e) const
void	extent (DataId di, double volume, double area, double perimeter)
void	process (const Eref &e, ProcPtr info)
void	reinit (const Eref &e, ProcPtr info)
void	triggerRemesh (const Eref &e, double oldvol, unsigned int startEntry, const vector< unsigned int > &localIndices, const vector< double > &vols)
Static Public Member Functions
static const Cinfo *	initCinfo ()

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Detailed Description

The MeshEntry is a single 'compartment' in the mathematical sense, that is, all properties are assumed homogenous within it. It is a FieldElement, so it gets all its values from the parent ChemCompt.

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Constructor & Destructor Documentation

MeshEntry::MeshEntry

(

)

MeshEntry::MeshEntry

(

const ChemCompt *

parent

)

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Member Function Documentation

void MeshEntry::extent	(	DataId	di,
		double	volume,
		double	area,
		double	perimeter
	)

vector< double > MeshEntry::getCoordinates

(

const Eref &

e

)

const

Coords that define current MeshEntry. Usually generated on the fly by passing the current Field Index to the parent ChemCompt subclass, which will figure it out.

References Eref::fieldIndex(), and ChemCompt::getCoordinates().

Referenced by initCinfo().

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vector< double > MeshEntry::getDiffusionArea

(

const Eref &

e

)

const

Diffusion scaling for area

References Eref::fieldIndex(), and ChemCompt::getDiffusionArea().

Referenced by initCinfo().

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vector< double > MeshEntry::getDiffusionScaling

(

const Eref &

e

)

const

Diffusion scaling for geometry of interface

References Eref::fieldIndex(), and ChemCompt::getDiffusionScaling().

Referenced by initCinfo().

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unsigned int MeshEntry::getDimensions

(

const Eref &

e

)

const

returns number of dimension

References Eref::fieldIndex(), and ChemCompt::getMeshDimensions().

Referenced by initCinfo().

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unsigned int MeshEntry::getMeshType

(

const Eref &

e

)

const

The MeshType defines the shape of the mesh entry. 0: Not assigned 1: cuboid 2: cylinder 3. cylindrical shell 4: cylindrical shell segment 5: sphere 6: spherical shell 7: spherical shell segment 8: Tetrahedral

References Eref::fieldIndex(), and ChemCompt::getMeshType().

Referenced by initCinfo().

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vector< unsigned int > MeshEntry::getNeighbors

(

const Eref &

e

)

const

Indices of other Entries that this one connects to, for diffusion

References Eref::fieldIndex(), and ChemCompt::getNeighbors().

Referenced by initCinfo().

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double MeshEntry::getVolume

(

const Eref &

e

)

const

References Eref::fieldIndex(), and ChemCompt::getMeshEntryVolume().

Referenced by initCinfo().

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const Cinfo * MeshEntry::initCinfo

(

)

[static]

References getCoordinates(), getDiffusionArea(), getDiffusionScaling(), getDimensions(), ValueFinfoBase::getFinfo(), getMeshType(), getNeighbors(), getVolume(), Neutral::initCinfo(), process(), and reinit().

Referenced by ChemCompt::initCinfo().

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void MeshEntry::process	(	const Eref &	e,
		ProcPtr	info
	)

Update the diffusion rate terms. Note that these stay the same through the entire clock tick, even if the GSL solver takes many intermediate steps. The assumption is that the concs change slowly enough that the diffusion terms are not hugely changed over the duration of one tick. Also assume that diffusion itself is slow. The latter assumption is OK for suitable grid sizes. The first assumption is OK with a sensible tick step.

Referenced by initCinfo().

void MeshEntry::reinit	(	const Eref &	e,
		ProcPtr	info
	)

Assigns the Stoich Id to the parent.

References Eref::dataIndex(), and Neutral::parent().

Referenced by initCinfo().

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void MeshEntry::triggerRemesh	(	const Eref &	e,
		double	oldvol,
		unsigned int	startEntry,
		const vector< unsigned int > &	localIndices,
		const vector< double > &	vols
	)

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

• mesh/MeshEntry.h
• mesh/MeshEntry.cpp