CylMesh Class Reference

#include <CylMesh.h>

Inheritance diagram for CylMesh:

Collaboration diagram for CylMesh:

Public Member Functions
	CylMesh ()
	~CylMesh ()
void	updateCoords (const Eref &e, const vector< double > &childConcs)
void	setX0 (const Eref &e, double v)
double	getX0 (const Eref &e) const
void	setY0 (const Eref &e, double v)
double	getY0 (const Eref &e) const
void	setZ0 (const Eref &e, double v)
double	getZ0 (const Eref &e) const
void	setR0 (const Eref &e, double v)
double	getR0 (const Eref &e) const
void	setX1 (const Eref &e, double v)
double	getX1 (const Eref &e) const
void	setY1 (const Eref &e, double v)
double	getY1 (const Eref &e) const
void	setZ1 (const Eref &e, double v)
double	getZ1 (const Eref &e) const
void	setR1 (const Eref &e, double v)
double	getR1 (const Eref &e) const
void	innerSetCoords (const Eref &e, const vector< double > &v)
void	setCoords (const Eref &e, vector< double > v)
vector< double >	getCoords (const Eref &e) const
void	setDiffLength (const Eref &e, double v)
double	getDiffLength (const Eref &e) const
double	getTotLength () const
unsigned int	innerGetDimensions () const
unsigned int	getMeshType (unsigned int fid) const
	Virtual function to return MeshType of specified entry.
unsigned int	getMeshDimensions (unsigned int fid) const
	Virtual function to return dimensions of specified entry.
double	getMeshEntryVolume (unsigned int fid) const
	Virtual function to return volume of mesh Entry.
vector< double >	getCoordinates (unsigned int fid) const
	Virtual function to return coords of mesh Entry.
vector< double >	getDiffusionArea (unsigned int fid) const
	Virtual function to return diffusion X-section area.
vector< double >	getDiffusionScaling (unsigned int fid) const
	Virtual function to return scale factor for diffusion. 1 here.
double	extendedMeshEntryVolume (unsigned int fid) const
	Volume of mesh Entry including abutting diff-coupled voxels.
unsigned int	innerGetNumEntries () const
void	innerSetNumEntries (unsigned int n)
	Inherited virtual func.
vector< unsigned int >	getParentVoxel () const
	Inherited virtual, do nothing for now.
const vector< double > &	vGetVoxelVolume () const
	Virtual func so that derived classes can pass voxel volume back.
const vector< double > &	vGetVoxelMidpoint () const
	Virtual func so that derived classes can return voxel midpoint.
const vector< double > &	getVoxelArea () const
const vector< double > &	getVoxelLength () const
double	vGetEntireVolume () const
	Inherited virtual. Returns entire volume of compartment.
bool	vSetVolumeNotRates (double volume)
	Inherited virtual. Resizes len and dia of each voxel.
void	innerBuildDefaultMesh (const Eref &e, double volume, unsigned int numEntries)
	Virtual func to make a mesh with specified Volume and numEntries.
void	innerHandleRequestMeshStats (const Eref &e, const SrcFinfo2< unsigned int, vector< double > > *meshStatsFinfo)
void	innerHandleNodeInfo (const Eref &e, unsigned int numNodes, unsigned int numThreads)
void	transmitChange (const Eref &e)
void	buildStencil ()
void	matchMeshEntries (const ChemCompt *other, vector< VoxelJunction > &ret) const
double	nearest (double x, double y, double z, unsigned int &index) const
double	nearest (double x, double y, double z, double &linePos, double &r) const
void	indexToSpace (unsigned int index, double &x, double &y, double &z) const
void	matchCylMeshEntries (const CylMesh *other, vector< VoxelJunction > &ret) const
void	matchCubeMeshEntries (const CubeMesh *other, vector< VoxelJunction > &ret) const
void	matchNeuroMeshEntries (const NeuroMesh *other, vector< VoxelJunction > &ret) const
double	selectGridVolume (double h) const
Static Public Member Functions
static const Cinfo *	initCinfo ()

Detailed Description

The CylMesh represents a chemically identified compartment shaped like an extended cylinder. This is psuedo-1 dimension: Only the axial dimension is considered for diffusion and subdivisions. Typically used in modelling small segments of dendrite

Constructor & Destructor Documentation

CylMesh::CylMesh ( )

CylMesh::~CylMesh ( )

Member Function Documentation

void CylMesh::buildStencil ( )

References MeshCompt::addRow(), MeshCompt::innerResetStencil(), PI, and MeshCompt::setStencilSize().

Referenced by innerSetNumEntries().

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double CylMesh::extendedMeshEntryVolume ( unsigned int fid ) const [virtual]

Volume of mesh Entry including abutting diff-coupled voxels.

Virtual function to return volume of mesh Entry, including for diffusively coupled voxels from other solvers.

Reimplemented from MeshCompt.

References getMeshEntryVolume().

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vector< double > CylMesh::getCoordinates ( unsigned int fid ) const [virtual]

Virtual function to return coords of mesh Entry.

Virtual function to return coords of mesh Entry. For Cylindrical mesh, coords are x1y1z1 x2y2z2 r0 r1 phi0 phi1

Implements ChemCompt.

vector< double > CylMesh::getCoords ( const Eref & e ) const

Referenced by initCinfo().

double CylMesh::getDiffLength ( const Eref & e ) const

Referenced by initCinfo().

vector< double > CylMesh::getDiffusionArea ( unsigned int fid ) const [virtual]

Virtual function to return diffusion X-section area.

Virtual function to return diffusion X-section area for each neighbor.

Implements ChemCompt.

References PI.

vector< double > CylMesh::getDiffusionScaling ( unsigned int fid ) const [virtual]

Virtual function to return scale factor for diffusion. 1 here.

Implements ChemCompt.

unsigned int CylMesh::getMeshDimensions ( unsigned int fid ) const [virtual]

Virtual function to return dimensions of specified entry.

Implements ChemCompt.

double CylMesh::getMeshEntryVolume ( unsigned int fid ) const [virtual]

Virtual function to return volume of mesh Entry.

diffLength = length constant for diffusive spread len = length of each mesh entry totLen = total length of cylinder diffLength = k * r^2 Each entry has the same number of diffLengths, L = len/diffLength. Thinner entries have shorter diffLength. This gives a moderately nasty quadratic. However, as len(i) is prop to diffLength(i), and diffLength(i) is prop to r(i)^2 and the cyl-mesh is assumed a gently sloping cone we get len(i) is prop to (r0 + slope.x)^2 and ignoring the 2nd-order term we have len(i) is approx proportional to x position.

dr/dx = (r1-r0)/len ri = r0 + i * dr/dx r(i+1)-ri = (r1-r0)/numEntries len = k * r^2 we get k from integ_r0,r1( len.dr ) = totLen So k.r^3/3 | r0, r1 = totLen => k/3 * ( r1^3 - r0^3) = totLen => k = 3 * totLen / (r1^3 - r0^3); This is bad if r1 == r0, and is generally unpleasant.

Simple definition of rSlope: rSlope is measured per meshEntry, not per length: rSlope = ( r1 - r0 ) / numEntries; Let's just compute len0 from r0 and diffLength. len0/diffLength = 2 * r0 / (r0 + r1) so len0 = diffLength * 2 * r0 / (r0 + r1) and dlen/dx = lenSlope = diffLength * rSlope * 2/(r0 + r1)

Drop the following calculations: // dlen/dx = dr/dx * dlen/dr = ( (r1-r0)/len ) * 2k.r // To linearize, let 2r = r0 + r1. // so dlen/dx = ( (r1-r0)/len ) * k * ( r0 + r1 ) // len(i) = len0 + i * dlen/dx // len0 = totLen/numEntries - ( numEntries/2 ) * dlen/dx

Implements ChemCompt.

References PI.

Referenced by extendedMeshEntryVolume(), vGetEntireVolume(), and vGetVoxelVolume().

unsigned int CylMesh::getMeshType ( unsigned int fid ) const [virtual]

Virtual function to return MeshType of specified entry.

Implements ChemCompt.

References CYL, and SPHERE_SHELL_SEG.

vector< unsigned int > CylMesh::getParentVoxel ( ) const [virtual]

Inherited virtual, do nothing for now.

Implements MeshCompt.

double CylMesh::getR0 ( const Eref & e ) const

Referenced by initCinfo().

double CylMesh::getR1 ( const Eref & e ) const

Referenced by initCinfo().

double CylMesh::getTotLength ( ) const

Referenced by initCinfo().

const vector< double > & CylMesh::getVoxelArea ( ) const [virtual]

Implements MeshCompt.

References PI.

const vector< double > & CylMesh::getVoxelLength ( ) const [virtual]

Implements MeshCompt.

double CylMesh::getX0 ( const Eref & e ) const

Referenced by initCinfo().

double CylMesh::getX1 ( const Eref & e ) const

Referenced by initCinfo().

double CylMesh::getY0 ( const Eref & e ) const

Referenced by initCinfo().

double CylMesh::getY1 ( const Eref & e ) const

Referenced by initCinfo().

double CylMesh::getZ0 ( const Eref & e ) const

Referenced by initCinfo().

double CylMesh::getZ1 ( const Eref & e ) const

Referenced by initCinfo().

void CylMesh::indexToSpace	(	unsigned int	index,
		double &	x,
		double &	y,
		double &	z
	)			const `[virtual]`

Converts specified index to xyz coords of middle of voxel Values out of range return original xyz

Implements ChemCompt.

const Cinfo * CylMesh::initCinfo ( ) [static]

Reimplemented from ChemCompt.

References getCoords(), getDiffLength(), getR0(), getR1(), getTotLength(), getX0(), getX1(), getY0(), getY1(), getZ0(), getZ1(), ChemCompt::initCinfo(), innerGetNumEntries(), setCoords(), setDiffLength(), setR0(), setR1(), setX0(), setX1(), setY0(), setY1(), setZ0(), and setZ1().

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void CylMesh::innerBuildDefaultMesh	(	const Eref &	e,
		double	volume,
		unsigned int	numEntries
	)			`[virtual]`

Virtual func to make a mesh with specified Volume and numEntries.

Single voxel cylinder with diameter = length. vol = volume = pi.r^2.len. So len = 2r, volume = pi*r^2*2r = 2pi*r^3 so r = (volume/2pi)^(1/3)

Implements ChemCompt.

References PI, and setCoords().

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unsigned int CylMesh::innerGetDimensions ( ) const [virtual]

Implements ChemCompt.

unsigned int CylMesh::innerGetNumEntries ( ) const [virtual]

Inherited virtual func. Returns number of MeshEntry in array

Implements ChemCompt.

Referenced by initCinfo().

void CylMesh::innerHandleNodeInfo	(	const Eref &	e,
		unsigned int	numNodes,
		unsigned int	numThreads
	)			`[virtual]`

Implements ChemCompt.

void CylMesh::innerHandleRequestMeshStats	(	const Eref &	e,
		const SrcFinfo2< unsigned int, vector< double > > *	meshStatsFinfo
	)

void CylMesh::innerSetCoords	(	const Eref &	e,
		const vector< double > &	v
	)

Referenced by testCubeMeshJunctionDiffSizeMesh(), and testCubeMeshJunctionTwoDimSurface().

void CylMesh::innerSetNumEntries ( unsigned int n ) [virtual]

Inherited virtual func.

Inherited virtual func. Assigns number of MeshEntries.

Implements ChemCompt.

References buildStencil().

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void CylMesh::matchCubeMeshEntries	(	const CubeMesh *	other,
		vector< VoxelJunction > &	ret
	)			const

void CylMesh::matchCylMeshEntries	(	const CylMesh *	other,
		vector< VoxelJunction > &	ret
	)			const

void CylMesh::matchMeshEntries	(	const ChemCompt *	other,
		vector< VoxelJunction > &	ret
	)			const

void CylMesh::matchNeuroMeshEntries	(	const NeuroMesh *	other,
		vector< VoxelJunction > &	ret
	)			const

double CylMesh::nearest	(	double	x,
		double	y,
		double	z,
		double &	linePos,
		double &	r
	)			const

References ChemCompt::distance().

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double CylMesh::nearest	(	double	x,
		double	y,
		double	z,
		unsigned int &	index
	)			const `[virtual]`

Returns distance and index of nearest mesh entry. Computes each mesh entry position as its geometric centre. If the current location is not inside a valid mesh entry, distance returned is negative.

Implements ChemCompt.

double CylMesh::selectGridVolume ( double h ) const