#include <CylMesh.h>

Inheritance diagram for CylMesh:

Collaboration diagram for CylMesh:

Public Member Functions
void	buildStencil ()

	CylMesh ()

double	extendedMeshEntryVolume (unsigned int fid) const
	Volume of mesh Entry including abutting diff-coupled voxels. More...

vector< double >	getCoordinates (unsigned int fid) const
	Virtual function to return coords of mesh Entry. More...

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

double	getDiffLength (const Eref &e) const

vector< double >	getDiffusionArea (unsigned int fid) const
	Virtual function to return diffusion X-section area. More...

vector< double >	getDiffusionScaling (unsigned int fid) const
	Virtual function to return scale factor for diffusion. 1 here. More...

unsigned int	getMeshDimensions (unsigned int fid) const
	Virtual function to return dimensions of specified entry. More...

double	getMeshEntryVolume (unsigned int fid) const
	Virtual function to return volume of mesh Entry. More...

unsigned int	getMeshType (unsigned int fid) const
	Virtual function to return MeshType of specified entry. More...

vector< unsigned int >	getParentVoxel () const
	Inherited virtual, do nothing for now. More...

double	getR0 (const Eref &e) const

double	getR1 (const Eref &e) const

double	getTotLength () const

const vector< double > &	getVoxelArea () const

const vector< double > &	getVoxelLength () const

double	getX0 (const Eref &e) const

double	getX1 (const Eref &e) const

double	getY0 (const Eref &e) const

double	getY1 (const Eref &e) const

double	getZ0 (const Eref &e) const

double	getZ1 (const Eref &e) const

void	indexToSpace (unsigned int index, double &x, double &y, double &z) const

void	innerBuildDefaultMesh (const Eref &e, double volume, unsigned int numEntries)
	Virtual func to make a mesh with specified Volume and numEntries. More...

unsigned int	innerGetDimensions () const

unsigned int	innerGetNumEntries () const

void	innerHandleNodeInfo (const Eref &e, unsigned int numNodes, unsigned int numThreads)

void	innerHandleRequestMeshStats (const Eref &e, const SrcFinfo2< unsigned int, vector< double > > *meshStatsFinfo)
	More inherited virtual funcs: request comes in for mesh stats. More...

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

void	innerSetNumEntries (unsigned int n)
	Inherited virtual func. More...

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

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

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

void	matchNeuroMeshEntries (const NeuroMesh *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

double	selectGridVolume (double h) const

void	setCoords (const Eref &e, vector< double > v)

void	setDiffLength (const Eref &e, double v)

void	setR0 (const Eref &e, double v)

void	setR1 (const Eref &e, double v)

void	setX0 (const Eref &e, double v)

void	setX1 (const Eref &e, double v)

void	setY0 (const Eref &e, double v)

void	setY1 (const Eref &e, double v)

void	setZ0 (const Eref &e, double v)

void	setZ1 (const Eref &e, double v)

void	transmitChange (const Eref &e)

void	updateCoords (const Eref &e, const vector< double > &childConcs)

double	vGetEntireVolume () const
	Inherited virtual. Returns entire volume of compartment. More...

const vector< double > &	vGetVoxelMidpoint () const
	Virtual func so that derived classes can return voxel midpoint. More...

const vector< double > &	vGetVoxelVolume () const
	Virtual func so that derived classes can pass voxel volume back. More...

bool	vSetVolumeNotRates (double volume)
	Inherited virtual. Resizes len and dia of each voxel. More...

	~CylMesh ()

Public Member Functions inherited from MeshCompt
void	addRow (unsigned int index, const vector< double > &entry, const vector< unsigned int > &colIndex)

void	clearExtendedMeshEntryVolume ()
	Inherited virtual function to clear the vector of MeshEntryVolume. More...

double	extendedMeshEntryVolume (unsigned int fid) const
	Virtual function to return volume of mesh Entry, including. More...

void	extendStencil (const ChemCompt *other, const vector< VoxelJunction > &vj)
	Add boundary voxels to stencil for cross-solver junctions. More...

vector< unsigned int >	getNeighbors (unsigned int fid) const
	Looks up stencil to return vector of indices of coupled voxels. More...

const SparseMatrix< double > &	getStencil () const
	Returns entire sparse matrix of mesh. Used by diffusion solver. More...

unsigned int	getStencilRow (unsigned int meshIndex, const double entry, const unsigned int colIndex) const

vector< double >	innerGetStencilRate (unsigned int row) const

void	innerResetStencil ()
	virtual func implemented here. More...

	MeshCompt ()

void	setStencilSize (unsigned int numRows, unsigned int numCols)

	~MeshCompt ()

Public Member Functions inherited from ChemCompt
void	buildDefaultMesh (const Eref &e, double volume, unsigned int numEntries)

void	buildJunction (ChemCompt *other, vector< VoxelJunction > &ret)

	ChemCompt ()

void	flipRet (vector< VoxelJunction > &ret) const
	Utility function for swapping first and second in VoxelJunctions. More...

void	getChildConcs (const Eref &e, vector< double > &childConcs) const

unsigned int	getDimensions () const

double	getEntireVolume (const Eref &e) const

bool	getIsMembraneBound () const

string	getMethod () const

unsigned int	getNumEntries () const

double	getOneVoxelVolume (const Eref &e, unsigned int voxel) const

vector< unsigned int >	getStencilIndex (unsigned int row) const

vector< double >	getStencilRate (unsigned int row) const

vector< double >	getVoxelMidpoint () const
	Returns vector of all voxel midpoints in compartment. More...

vector< double >	getVoxelVolume () const
	Returns vector of all voxel volumes in compartment. More...

void	handleNodeInfo (const Eref &e, unsigned int numNodes, unsigned int numThreads)

MeshEntry *	lookupEntry (unsigned int index)

void	resetStencil ()

unsigned int	setChildConcs (const Eref &e, const vector< double > &childConcs, unsigned int start) const

void	setEntireVolume (const Eref &e, double volume)

void	setIsMembraneBound (bool v)

virtual void	setMeshEntryVolume (unsigned int fid, double volume)

void	setMethod (string method)

void	setNumEntries (unsigned int num)

void	setOneVoxelVolume (const Eref &e, unsigned int voxel, double volume)

void	setVolumeNotRates (double volume)

virtual	~ChemCompt ()

Static Public Member Functions
static const Cinfo *	initCinfo ()

Static Public Member Functions inherited from ChemCompt
static double	distance (double x, double y, double z)

static const Cinfo *	initCinfo ()

static SrcFinfo1< vector < double > > *	voxelVolOut ()

Private Attributes
double	diffLength_
	Radius at other end. More...

bool	isToroid_

double	lenSlope_
	Utility value: dr/dx. More...

unsigned int	numEntries_

double	r0_
	coords More...

double	r1_
	Radius at one end. More...

double	rSlope_
	Utility value: Total length of cylinder. More...

double	surfaceGranularity_
	Length constant for diffusion. Equal to dx. More...

double	totLen_

bool	useCaps_

double	x0_

double	x1_
	coords More...

double	y0_
	coords More...

double	y1_
	coords More...

double	z0_
	coords More...

double	z1_
	coords More...

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

Definition at line 19 of file CylMesh.h.

Constructor & Destructor Documentation

CylMesh::CylMesh ( )

Definition at line 169 of file CylMesh.cpp.

     :
         numEntries_( 100 ),
         useCaps_( 0 ),
         isToroid_( false ),
         x0_( 0.0 ),
         y0_( 0.0 ),
         z0_( 0.0 ),
         x1_( 100.0e-6 ),
         y1_( 0.0 ),
         z1_( 0.0 ),
         r0_( 1.0e-6 ),
         r1_( 1.0e-6 ),
         diffLength_( 1.0e-6 ),
         surfaceGranularity_( 0.1 ),
         totLen_( 100.0e-6 ),
         rSlope_( 0.0 ),
         lenSlope_( 0.0 )
 {
     ;
 }

CylMesh::~CylMesh ( )

Definition at line 191 of file CylMesh.cpp.

 {
     ;
 }

Member Function Documentation

void CylMesh::buildStencil ( )

Definition at line 785 of file CylMesh.cpp.

References MeshCompt::addRow(), diffLength_, MeshCompt::innerResetStencil(), isToroid_, numEntries_, PI, r0_, r1_, rSlope_, and MeshCompt::setStencilSize().

Referenced by innerSetNumEntries(), and updateCoords().

 {
     setStencilSize( numEntries_, numEntries_ );
     for ( unsigned int i = 0; i < numEntries_; ++i ) {
         double rLow = r0_ + i * rSlope_;
         double rHigh = r0_ + (i + 1.0) * rSlope_;
         double aLow = rLow * rLow * PI;
         double aHigh = rHigh * rHigh * PI;
         vector< double > entry;
         vector< unsigned int > colIndex;
         if ( i == 0 ) {
             colIndex.push_back( 1 );
             entry.push_back( aHigh / diffLength_ );
             if ( isToroid_ ) {
                 colIndex.push_back( numEntries_ - 1 );
                 entry.push_back( aLow / diffLength_ );
             }
         } else if ( i == numEntries_ - 1 ) {
             if ( isToroid_ ) {
                 colIndex.push_back( 0 );
                 if ( r0_ < r1_ )
                     entry.push_back( r0_ * r0_ * PI / diffLength_ );
                 else
                     entry.push_back( r1_ * r1_ * PI / diffLength_ );
             }
             colIndex.push_back( numEntries_ - 2 );
             entry.push_back( aLow / diffLength_ );
         } else { // Mostly it is in the middle.
             colIndex.push_back( i - 1 );
             entry.push_back( aLow / diffLength_ );
             colIndex.push_back( i + 1 );
             entry.push_back( aHigh / diffLength_ );
         }
         addRow( i, entry, colIndex );
     }
     innerResetStencil();
 }

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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.

Implements ChemCompt.

Definition at line 569 of file CylMesh.cpp.

References MeshCompt::extendedMeshEntryVolume(), getMeshEntryVolume(), and numEntries_.

 {
     if ( fid < numEntries_ ) {
         return getMeshEntryVolume( fid );
     } else {
         return MeshCompt::extendedMeshEntryVolume( fid - numEntries_ );
     }
 }

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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.

Definition at line 489 of file CylMesh.cpp.

References diffLength_, lenSlope_, r0_, r1_, rSlope_, totLen_, x0_, x1_, y0_, y1_, z0_, and z1_.

 {
     vector< double > ret(10, 0.0);
     double len0 = diffLength_ * 2 * r0_ / ( r0_ + r1_ );
     // double len0 = diffLength_ * 2 * ( r0_ + rSlope_ / 0.5) / ( r0_ + r1_ );
     double lenStart = len0 + lenSlope_ * 0.5;
 
     double axialStart = fid * lenStart + ( ( fid * (fid - 1 ) )/2 ) * lenSlope_;
         // fid * totLen_/numEntries_ + (fid - frac ) * lenSlope_;
     double axialEnd =
         (fid + 1) * lenStart + ( ( fid * (fid + 1 ) )/2 ) * lenSlope_;
         // (fid + 1) * totLen_/numEntries_ + (fid - frac + 1.0) * lenSlope_;
 
     ret[0] = x0_ + (x1_ - x0_ ) * axialStart/totLen_;
     ret[1] = y0_ + (y1_ - y0_ ) * axialStart/totLen_;
     ret[2] = z0_ + (z1_ - z0_ ) * axialStart/totLen_;
 
     ret[3] = x0_ + (x1_ - x0_ ) * axialEnd/totLen_;
     ret[4] = y0_ + (y1_ - y0_ ) * axialEnd/totLen_;
     ret[5] = z0_ + (z1_ - z0_ ) * axialEnd/totLen_;
 
     ret[6] = r0_ + fid * rSlope_;
     ret[7] = r0_ + (fid + 1.0) * rSlope_;
 
     ret[8] = 0;
     ret[9] = 0;
 
     return ret;
 }

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

Definition at line 372 of file CylMesh.cpp.

References diffLength_, r0_, r1_, x0_, x1_, y0_, y1_, z0_, and z1_.

Referenced by initCinfo().

 {
     vector< double > ret( 9 );
 
     ret[0] = x0_;
     ret[1] = y0_;
     ret[2] = z0_;
 
     ret[3] = x1_;
     ret[4] = y1_;
     ret[5] = z1_;
 
     ret[6] = r0_;
     ret[7] = r1_;
 
     ret[8] = diffLength_;
     return ret;
 }

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

Definition at line 400 of file CylMesh.cpp.

References diffLength_.

Referenced by initCinfo().

 {
     return diffLength_;
 }

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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.

Definition at line 520 of file CylMesh.cpp.

References isToroid_, numEntries_, PI, r0_, and rSlope_.

 {
     if ( numEntries_ <= 1 )
         return vector< double >( 0 );
 
     double rlow = r0_ + fid * rSlope_;
     double rhigh = r0_ + (fid + 1.0) * rSlope_;
 
     if ( fid == 0 ) {
         if ( isToroid_ ) {
             vector < double > ret( 2 );
             ret[0] = rlow * rlow * PI;
             ret[1] = rhigh * rhigh * PI;
             return ret;
         } else {
             return vector < double >( 1, rhigh * rhigh * PI );
         }
     }
 
     if ( fid == (numEntries_ - 1 ) ) {
         if ( isToroid_ ) {
             vector < double > ret( 2 );
             ret[0] = rlow * rlow * PI;
             ret[1] = r0_ * r0_ * PI; // Wrapping around
             return ret;
         } else {
             return vector < double >( 1, rlow * rlow * PI );
         }
     }
     vector< double > ret( 2 );
     ret[0] = rlow * rlow * PI;
     ret[1] = rhigh * rhigh * PI;
     return ret;
 }

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

virtual

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

Implements ChemCompt.

Definition at line 556 of file CylMesh.cpp.

References isToroid_, and numEntries_.

 {
     if ( numEntries_ <= 1 )
         return vector< double >( 0 );
 
     if ( !isToroid_ && ( fid == 0 || fid == (numEntries_ - 1) ) )
         return vector< double >( 1, 1.0 );
 
     return vector< double >( 2, 1.0 );
 }

unsigned int CylMesh::getMeshDimensions ( unsigned int fid ) const

virtual

Virtual function to return dimensions of specified entry.

Implements ChemCompt.

Definition at line 430 of file CylMesh.cpp.

 {
     return 3;
 }

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.

Definition at line 477 of file CylMesh.cpp.

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

 {
     double len0 = diffLength_ * 2 * r0_ / ( r0_ + r1_ );
 
     double ri = r0_ + (fid + 0.5) * rSlope_;
     double leni = len0 + ( fid + 0.5 ) * lenSlope_;
 
     return leni * ri * ri * PI;
 }

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unsigned int CylMesh::getMeshType ( unsigned int fid ) const

virtual

Virtual function to return MeshType of specified entry.

Implements ChemCompt.

Definition at line 421 of file CylMesh.cpp.

References CYL, isToroid_, numEntries_, SPHERE_SHELL_SEG, and useCaps_.

 {
     if ( !isToroid_ && useCaps_ && ( fid == 0 || fid == numEntries_ - 1 ) )
         return SPHERE_SHELL_SEG;
 
     return CYL;
 }

vector< unsigned int > CylMesh::getParentVoxel ( ) const

virtual

Inherited virtual, do nothing for now.

Implements MeshCompt.

Definition at line 656 of file CylMesh.cpp.

References numEntries_.

 {
     vector< unsigned int > ret( numEntries_ );
     if ( numEntries_ > 0 )
         ret[0] = static_cast< unsigned int >( -1 );
     for (unsigned int i = 1; i < numEntries_; ++i )
         ret[i] = i-1;
 
     return ret;
 }

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

Definition at line 285 of file CylMesh.cpp.

References r0_.

Referenced by initCinfo().

 {
     return r0_;
 }

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

Definition at line 338 of file CylMesh.cpp.

References r1_.

Referenced by initCinfo().

 {
     return r1_;
 }

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double CylMesh::getTotLength ( ) const

Definition at line 406 of file CylMesh.cpp.

References totLen_.

Referenced by initCinfo().

 {
     return totLen_;
 }

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const vector< double > & CylMesh::getVoxelArea ( ) const

virtual

Implements MeshCompt.

Definition at line 694 of file CylMesh.cpp.

References numEntries_, PI, r0_, and r1_.

 {
     static vector< double > area;
     area.resize( numEntries_ );
     for ( unsigned int i = 0; i < numEntries_; ++i ) {
         double frac = ( 0.5 + static_cast< double >( i ) ) /
             static_cast< double >( numEntries_ );
         double r = r0_ * ( 1.0 - frac ) + r1_ * frac;
         area[i] = r * r * PI;
     }
     return area;
 }

const vector< double > & CylMesh::getVoxelLength ( ) const

virtual

Implements MeshCompt.

Definition at line 707 of file CylMesh.cpp.

References numEntries_, and totLen_.

 {
     static vector< double > length;
     length.assign( numEntries_, totLen_ / numEntries_ );
     return length;
 }

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

Definition at line 246 of file CylMesh.cpp.

References x0_.

Referenced by initCinfo().

 {
     return x0_;
 }

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

Definition at line 299 of file CylMesh.cpp.

References x1_.

Referenced by initCinfo().

 {
     return x1_;
 }

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

Definition at line 259 of file CylMesh.cpp.

References y0_.

Referenced by initCinfo().

 {
     return y0_;
 }

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

Definition at line 312 of file CylMesh.cpp.

References y1_.

Referenced by initCinfo().

 {
     return y1_;
 }

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

Definition at line 272 of file CylMesh.cpp.

References z0_.

Referenced by initCinfo().

 {
     return z0_;
 }

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

Definition at line 325 of file CylMesh.cpp.

References z1_.

Referenced by initCinfo().

 {
     return z1_;
 }

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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.

Definition at line 1026 of file CylMesh.cpp.

References numEntries_, x0_, x1_, y0_, y1_, z0_, and z1_.

 {
     if ( index < numEntries_ ) {
         double k = ( index + 0.5 ) / static_cast< double >( numEntries_ );
         x = ( x1_ - x0_ ) * k + x0_;
         y = ( y1_ - y0_ ) * k + y0_;
         z = ( z1_ - z0_ ) * k + z0_;
     }
 }

const Cinfo * CylMesh::initCinfo ( )

static

Definition at line 27 of file CylMesh.cpp.

References cylMeshCinfo, 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().

 {
         // Field Definitions
         static ElementValueFinfo< CylMesh, double > x0(
             "x0",
             "x coord of one end",
             &CylMesh::setX0,
             &CylMesh::getX0
         );
         static ElementValueFinfo< CylMesh, double > y0(
             "y0",
             "y coord of one end",
             &CylMesh::setY0,
             &CylMesh::getY0
         );
         static ElementValueFinfo< CylMesh, double > z0(
             "z0",
             "z coord of one end",
             &CylMesh::setZ0,
             &CylMesh::getZ0
         );
         static ElementValueFinfo< CylMesh, double > r0(
             "r0",
             "Radius of one end",
             &CylMesh::setR0,
             &CylMesh::getR0
         );
         static ElementValueFinfo< CylMesh, double > x1(
             "x1",
             "x coord of other end",
             &CylMesh::setX1,
             &CylMesh::getX1
         );
         static ElementValueFinfo< CylMesh, double > y1(
             "y1",
             "y coord of other end",
             &CylMesh::setY1,
             &CylMesh::getY1
         );
         static ElementValueFinfo< CylMesh, double > z1(
             "z1",
             "z coord of other end",
             &CylMesh::setZ1,
             &CylMesh::getZ1
         );
         static ElementValueFinfo< CylMesh, double > r1(
             "r1",
             "Radius of other end",
             &CylMesh::setR1,
             &CylMesh::getR1
         );
         static ElementValueFinfo< CylMesh, vector< double > > coords(
             "coords",
             "All the coords as a single vector: x0 y0 z0  x1 y1 z1  r0 r1 diffLength",
             &CylMesh::setCoords,
             &CylMesh::getCoords
         );
 
         static ElementValueFinfo< CylMesh, double > diffLength(
             "diffLength",
             "Length constant to use for subdivisions"
             "The system will attempt to subdivide using compartments of"
             "length diffLength on average. If the cylinder has different end"
             "diameters r0 and r1, it will scale to smaller lengths"
             "for the smaller diameter end and vice versa."
             "Once the value is set it will recompute diffLength as "
             "totLength/numEntries",
             &CylMesh::setDiffLength,
             &CylMesh::getDiffLength
         );
 
         static ReadOnlyValueFinfo< CylMesh, unsigned int > numDiffCompts(
             "numDiffCompts",
             "Number of diffusive compartments in model",
             &CylMesh::innerGetNumEntries
         );
 
         static ReadOnlyValueFinfo< CylMesh, double > totLength(
             "totLength",
             "Total length of cylinder",
             &CylMesh::getTotLength
         );
 
         // MsgDest Definitions
 
         // Field Elements
 
     static Finfo* cylMeshFinfos[] = {
         &x0,            // Value
         &y0,            // Value
         &z0,            // Value
         &r0,            // Value
         &x1,            // Value
         &y1,            // Value
         &z1,            // Value
         &r1,            // Value
         &diffLength,            // Value
         &coords,        // Value
         &numDiffCompts,     // ReadOnlyValue
         &totLength,     // ReadOnlyValue
     };
 
     static string doc[] =
     {
         "Name", "CylMesh",
         "Author", "Upi Bhalla",
         "Description", "Chemical compartment with cylindrical geometry. "
                 "Defaults to a uniform cylinder of radius 1 micron, "
                 "length 100 microns, and voxel length 1 micron so there "
                 "are 100 voxels in the cylinder. "
                 "The cylinder can be given a linear taper, by assigning "
                 "different radii r0 and r1 to the two ends. ",
     };
     static Dinfo< CylMesh > dinfo;
     static Cinfo cylMeshCinfo (
         "CylMesh",
         ChemCompt::initCinfo(),
         cylMeshFinfos,
         sizeof( cylMeshFinfos ) / sizeof ( Finfo* ),
         &dinfo,
         doc,
         sizeof(doc)/sizeof(string)
     );
 
     return &cylMeshCinfo;
 }

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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.

Definition at line 641 of file CylMesh.cpp.

References numEntries, PI, and setCoords().

 {
     double r = pow( ( volume / ( PI * 2 ) ), 1.0 / 3 );
     vector< double > coords( 9, 0 );
     coords[3] = 2 * r;
     coords[6] = r;
     coords[7] = r;
     coords[8] = 2 * r / numEntries;
     setCoords( e, coords );
 }

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unsigned int CylMesh::innerGetDimensions ( ) const

virtual

Implements ChemCompt.

Definition at line 411 of file CylMesh.cpp.

 {
     return 3;
 }

unsigned int CylMesh::innerGetNumEntries ( ) const

virtual

Inherited virtual func. Returns number of MeshEntry in array

Implements ChemCompt.

Definition at line 615 of file CylMesh.cpp.

References numEntries_.

Referenced by initCinfo().

 {
     return numEntries_;
 }

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void CylMesh::innerHandleNodeInfo	(	const Eref &	e,
		unsigned int	numNodes,
		unsigned int	numThreads
	)

virtual

Implements ChemCompt.

Definition at line 591 of file CylMesh.cpp.

 {
         /*
     unsigned int numEntries = numEntries_;
     vector< double > vols( numEntries, volume_ / numEntries );
     vector< unsigned int > localEntries( numEntries );
     vector< vector< unsigned int > > outgoingEntries;
     vector< vector< unsigned int > > incomingEntries;
     */
     /*
     double oldvol = getMeshEntryVolume( 0 );
     meshSplit()->send( e,
         oldvol,
         vols, localEntries,
         outgoingEntries, incomingEntries );
         */
 }

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

More inherited virtual funcs: request comes in for mesh stats.

Definition at line 583 of file CylMesh.cpp.

References numEntries_, and vGetEntireVolume().

 {
     vector< double > ret( vGetEntireVolume() / numEntries_ ,1 );
     meshStatsFinfo->send( e, 1, ret );
 }

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

Definition at line 343 of file CylMesh.cpp.

References diffLength_, ChemCompt::getChildConcs(), r0_, r1_, updateCoords(), x0_, x1_, y0_, y1_, z0_, and z1_.

Referenced by setCoords().

 {
     vector< double > childConcs;
     getChildConcs( e, childConcs );
     x0_ = v[0];
     y0_ = v[1];
     z0_ = v[2];
 
     x1_ = v[3];
     y1_ = v[4];
     z1_ = v[5];
 
     r0_ = v[6];
     r1_ = v[7];
 
     diffLength_ = v[8];
 
     updateCoords( e, childConcs );
 }

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void CylMesh::innerSetNumEntries ( unsigned int n )

virtual

Inherited virtual func.

Inherited virtual func. Assigns number of MeshEntries.

Implements ChemCompt.

Definition at line 623 of file CylMesh.cpp.

References buildStencil(), diffLength_, lenSlope_, numEntries_, r0_, r1_, rSlope_, and totLen_.

 {
     static const unsigned int WayTooLarge = 1000000;
     if ( n == 0 || n > WayTooLarge ) {
         cout << "Warning: CylMesh::innerSetNumEntries( " << n <<
         " ): out of range\n";
         return;
     }
     assert( n > 0 );
     numEntries_ = n;
     diffLength_ = totLen_ / n;
     rSlope_ = ( r1_ - r0_ ) / numEntries_;
     lenSlope_ = diffLength_ * rSlope_ * 2 / ( r0_ + r1_ );
 
     buildStencil();
 }

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

Definition at line 983 of file CylMesh.cpp.

References Vec::a0(), Vec::a1(), Vec::a2(), diffLength_, EPSILON, fillPointsOnCircle(), CubeMesh::getDx(), ChemCompt::getNumEntries(), numEntries_, Vec::orthogonalAxes(), r0_, rSlope_, selectGridVolume(), totLen_, x0_, x1_, y0_, y1_, z0_, and z1_.

Referenced by matchMeshEntries().

 {
     const double EPSILON = 1e-18;
     Vec a( x1_ - x0_, y1_ - y0_, z1_ - z0_ );
     Vec u;
     Vec v;
     a.orthogonalAxes( u, v );
 
     double h = selectGridVolume( other->getDx() );
 
     unsigned int num = floor( 0.1 + diffLength_ / h );
     // March along axis of cylinder.
     // q is the location of the point along axis.
     for ( unsigned int i = 0; i < numEntries_; ++i ) {
         vector< double >area( other->getNumEntries(), 0.0 );
         for ( unsigned int j = 0; j < num; ++j ) {
             unsigned int m = i * num + j;
             double frac = ( m * h + h/2.0 ) / totLen_;
             double q0 = x0_ + a.a0() * frac;
             double q1 = y0_ + a.a1() * frac;
             double q2 = z0_ + a.a2() * frac;
             // get radius of cylinder at this point.
             double r = r0_ + ( m * h + h / 2.0 ) * rSlope_;
             fillPointsOnCircle( u, v, Vec( q0, q1, q2 ),
                         h, r, area, other );
             }
         // Go through all cubeMesh entries and compute diffusion
         // cross-section. Assume this is through a membrane, so the
         // only factor relevant is area. Not the distance.
         for ( unsigned int k = 0; k < area.size(); ++k ) {
             if ( area[k] > EPSILON ) {
                 ret.push_back( VoxelJunction( i, k, area[k] ) );
             }
         }
     }
 }

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

Definition at line 861 of file CylMesh.cpp.

References diffLength_, ChemCompt::distance(), EPSILON, getMeshEntryVolume(), numEntries_, PI, r0_, r1_, totLen_, x0_, x1_, y0_, y1_, z0_, and z1_.

Referenced by matchMeshEntries().

 {
     const double EPSILON = 1e-3;
     ret.clear();
     // Should really estimate the distance from the centre of the smaller
     // cylinder cap disk to the plane of the larger disk, provided it is
     // within the radius of the disk. The subsequent calculations are the
     // same though.
     double dr1 =    // startOfSelf-to-startOfOther
             distance(x0_ - other->x0_, y0_ - other->y0_, z0_ - other->z0_ );
     double dr2 =  // endOfSelf-to-endOfOther
             distance(x1_ - other->x1_, y1_ - other->y1_, z1_ - other->z1_ );
     double dr3 = // endOfSelf-to-startOfOther
             distance(x1_ - other->x0_, y1_ - other->y0_, z1_ - other->z0_ );
     double dr4 =  // startOfSelf-to-endOfOther
             distance(x0_ - other->x1_, y0_ - other->y1_, z0_ - other->z1_ );
 
     if ( dr1 <= dr2 && dr1 <= dr3 && dr1 <= dr4 ) {
         if ( ( dr1/totLen_ < EPSILON && dr1/other->totLen_ < EPSILON ) ) {
             double xda;
             if ( r0_ < other->r0_ )
                 xda = 2 * r0_ * r0_ * PI / ( diffLength_ + other->diffLength_ );
             else
                 xda = 2 * other->r0_ * other->r0_ * PI /
                         ( diffLength_ + other->diffLength_ );
             ret.push_back( VoxelJunction( 0, 0, xda ) );
             ret.back().first = 0;
             ret.back().second = 0;
             ret.back().firstVol = getMeshEntryVolume( 0 );
             ret.back().secondVol = other->getMeshEntryVolume( 0 );
         }
     } else if ( dr2 <= dr3 && dr2 <= dr4 ) {
         if ( ( dr2/totLen_ < EPSILON && dr2/other->totLen_ < EPSILON ) ) {
             double xda;
             if ( r1_ < other->r1_ )
                 xda = 2 * r1_ * r1_ * PI / ( diffLength_ + other->diffLength_ );
             else
                 xda = 2 * other->r1_ * other->r1_ * PI /
                         ( diffLength_ + other->diffLength_ );
             ret.push_back( VoxelJunction( numEntries_ - 1,
                         other->numEntries_ - 1, xda ) );
             ret.back().first = numEntries_;
             ret.back().second = other->numEntries_ - 1;
             ret.back().firstVol = getMeshEntryVolume( numEntries_ - 1 );
             ret.back().secondVol = other->getMeshEntryVolume( other->numEntries_ - 1 );
         }
     } else if ( dr3 <= dr4 ) {
         if ( ( dr3/totLen_ < EPSILON && dr3/other->totLen_ < EPSILON ) ) {
             double xda;
             if ( r1_ < other->r0_ )
                 xda = 2 * r1_ * r1_ * PI / ( diffLength_ + other->diffLength_ );
             else
                 xda = 2 * other->r0_ * other->r0_ * PI /
                         ( diffLength_ + other->diffLength_ );
             ret.push_back( VoxelJunction( numEntries_ - 1, 0, xda ) );
             ret.back().first = numEntries_ - 1;
             ret.back().second = 0;
             ret.back().firstVol = getMeshEntryVolume( numEntries_ - 1 );
             ret.back().secondVol = other->getMeshEntryVolume( 0 );
         }
     } else {
         if ( ( dr4/totLen_ < EPSILON && dr4/other->totLen_ < EPSILON ) ) {
             double xda;
             if ( r0_ < other->r1_ )
                 xda = 2 * r0_ * r0_ * PI / ( diffLength_ + other->diffLength_ );
             else
                 xda = 2 * other->r1_ * other->r1_ * PI /
                         ( diffLength_ + other->diffLength_ );
             ret.push_back( VoxelJunction( 0, other->numEntries_ - 1, xda ));
             ret.back().first = 0;
             ret.back().second = other->numEntries_ - 1;
             ret.back().firstVol = getMeshEntryVolume( 0 );
             ret.back().secondVol = other->getMeshEntryVolume( other->numEntries_ - 1 );
         }
     }
 }

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

virtual

Returns the meshIndices (NOT spatial indices) of all adjacent mesh entry pairs on ether side of the (self, other) junction. meshIndices are the indices that look up entries in the vector of pools. spatialIndices are (iz * ny + iy) * nx + ix, that is, a linear conversion of cartesian spatial indices. So, for two touching cubes, the return vector is the paired meshIndices on either side of the plane of contact. If one mesh has a finer mesh than the other, or if there are more than one contact points from self to other (for example, at a corner), then we just have multiple pairs using the same meshIndex of the repeated voxel.

Implements ChemCompt.

Definition at line 827 of file CylMesh.cpp.

References ChemCompt::flipRet(), matchCubeMeshEntries(), matchCylMeshEntries(), EndoMesh::matchMeshEntries(), and matchNeuroMeshEntries().

 {
     // This is seriously ugly, and what virtual funcs were meant to handle.
     // Dirty hack for now.
     const CylMesh* cyl = dynamic_cast< const CylMesh* >( other );
     if ( cyl ) {
         matchCylMeshEntries( cyl, ret );
         return;
     }
     const EndoMesh* em = dynamic_cast< const EndoMesh* >( other );
     if ( em )
     {
         em->matchMeshEntries( this, ret );
         flipRet( ret );
         return;
     }
     const CubeMesh* cube = dynamic_cast< const CubeMesh* >( other );
     if ( cube ) {
         matchCubeMeshEntries( cube, ret );
         return;
     }
     const NeuroMesh* nm = dynamic_cast< const NeuroMesh* >( other );
     if ( nm ) {
         matchNeuroMeshEntries( nm, ret );
         return;
     }
     cout << "Warning:CylMesh::matchMeshEntries: "  << 
             " unknown mesh type\n";
 }

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

Definition at line 1021 of file CylMesh.cpp.

Referenced by matchMeshEntries().

1023 {

1024 }

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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.

Definition at line 1075 of file CylMesh.cpp.

References numEntries_, r0_, and rSlope_.

 {
     double k = 0.0;
     double r;
     double ret = nearest( x, y, z, k, r );
     if ( k < 0.0 ) {
         ret = -ret;
         index = 0;
     } else if ( k > 1.0 ) {
         ret = -ret;
         index = numEntries_ - 1;
     } else { // Inside length of cylinder, now is it inside radius?
         index = k * numEntries_;
         double ri = r0_ + (index + 0.5) * rSlope_;
         if ( ret > ri )
             ret = -ret;
     }
     return ret;
 }

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

Definition at line 1045 of file CylMesh.cpp.

References ChemCompt::distance(), dotprd(), numEntries_, r0_, rSlope_, x0_, x1_, y0_, y1_, z0_, and z1_.

 {
     // Consider r0 = x0,y0,z0 and r1 = x1, y1, z1, and r = x,y,z.
     // Fraction along cylinder = k
     //
     // Then, point p along line from r0 to r1 is
     // p = k( r0-r1) + r1.
     //
     // Solving,
     // k = (r0 - r1).(r - r1) / (|r0-r1|^2)
     //
 
     double dist = distance( x1_ - x0_, y1_ - y0_, z1_ - z0_ );
     double k = dotprd(
         x1_ - x0_, y1_ - y0_, z1_ - z0_,
         x - x0_, y - y0_, z - z0_ ) / ( dist * dist );
 
     // x2, y2, z2 are the coords of the nearest point.
     double x2 = k * (x1_ - x0_) + x0_;
     double y2 = k * (y1_ - y0_) + y0_;
     double z2 = k * (z1_ - z0_) + z0_;
 
     double ret = distance( x - x2, y - y2, z - z2 );
     linePos = k;
     r = r0_ + k * numEntries_ * rSlope_;
     return ret;
 }

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double CylMesh::selectGridVolume ( double h ) const

Definition at line 940 of file CylMesh.cpp.

References diffLength_, r0_, r1_, and surfaceGranularity_.

Referenced by matchCubeMeshEntries().

 {
     if ( h > diffLength_ )
         h = diffLength_;
     if ( h > r0_ )
         h = r0_;
     if ( h > r1_ )
         h = r1_;
     h *= surfaceGranularity_;
     unsigned int num = ceil( diffLength_ / h );
     h = diffLength_ / num;
 
     return h;
 }

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

Definition at line 363 of file CylMesh.cpp.

References innerSetCoords(), and transmitChange().

Referenced by initCinfo(), and innerBuildDefaultMesh().

 {
     if ( v.size() < 9 ) {
         cout << "CylMesh::setCoords: Warning: size of argument vec should be >= 9, was " << v.size() << endl;
     }
     innerSetCoords( e, v );
     transmitChange( e );
 }

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void CylMesh::setDiffLength	(	const Eref &	e,
		double	v
	)

Definition at line 392 of file CylMesh.cpp.

References diffLength_, ChemCompt::getChildConcs(), and updateCoords().

Referenced by initCinfo().

 {
     vector< double > childConcs;
     getChildConcs( e, childConcs );
     diffLength_ = v;
     updateCoords( e, childConcs );
 }

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void CylMesh::setR0	(	const Eref &	e,
		double	v
	)

Definition at line 277 of file CylMesh.cpp.

References ChemCompt::getChildConcs(), r0_, and updateCoords().

Referenced by initCinfo().

 {
     vector< double > childConcs;
     getChildConcs( e, childConcs );
     r0_ = v;
     updateCoords( e, childConcs );
 }

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void CylMesh::setR1	(	const Eref &	e,
		double	v
	)

Definition at line 330 of file CylMesh.cpp.

References ChemCompt::getChildConcs(), r1_, and updateCoords().

Referenced by initCinfo().

 {
     vector< double > childConcs;
     getChildConcs( e, childConcs );
     r1_ = v;
     updateCoords( e, childConcs );
 }

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void CylMesh::setX0	(	const Eref &	e,
		double	v
	)

Definition at line 238 of file CylMesh.cpp.

References ChemCompt::getChildConcs(), updateCoords(), and x0_.

Referenced by initCinfo().

 {
     vector< double > childConcs;
     getChildConcs( e, childConcs );
     x0_ = v;
     updateCoords( e, childConcs );
 }

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void CylMesh::setX1	(	const Eref &	e,
		double	v
	)

Definition at line 291 of file CylMesh.cpp.

References ChemCompt::getChildConcs(), updateCoords(), and x1_.

Referenced by initCinfo().

 {
     vector< double > childConcs;
     getChildConcs( e, childConcs );
     x1_ = v;
     updateCoords( e, childConcs );
 }

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void CylMesh::setY0	(	const Eref &	e,
		double	v
	)

Definition at line 251 of file CylMesh.cpp.

References ChemCompt::getChildConcs(), updateCoords(), and y0_.

Referenced by initCinfo().

 {
     vector< double > childConcs;
     getChildConcs( e, childConcs );
     y0_ = v;
     updateCoords( e, childConcs );
 }

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void CylMesh::setY1	(	const Eref &	e,
		double	v
	)

Definition at line 304 of file CylMesh.cpp.

References ChemCompt::getChildConcs(), updateCoords(), and y1_.

Referenced by initCinfo().

 {
     vector< double > childConcs;
     getChildConcs( e, childConcs );
     y1_ = v;
     updateCoords( e, childConcs );
 }

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void CylMesh::setZ0	(	const Eref &	e,
		double	v
	)

Definition at line 264 of file CylMesh.cpp.

References ChemCompt::getChildConcs(), updateCoords(), and z0_.

Referenced by initCinfo().

 {
     vector< double > childConcs;
     getChildConcs( e, childConcs );
     z0_ = v;
     updateCoords( e, childConcs );
 }

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void CylMesh::setZ1	(	const Eref &	e,
		double	v
	)

Definition at line 317 of file CylMesh.cpp.

References ChemCompt::getChildConcs(), updateCoords(), and z1_.

Referenced by initCinfo().

 {
     vector< double > childConcs;
     getChildConcs( e, childConcs );
     z1_ = v;
     updateCoords( e, childConcs );
 }

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void CylMesh::transmitChange ( const Eref & e )

Definition at line 741 of file CylMesh.cpp.

Referenced by setCoords().

 {
         /*
     Id meshEntry( e.id().value() + 1 );
     assert(
         meshEntry.eref().data() == reinterpret_cast< char* >( lookupEntry( 0 ) )
     );
     double oldvol = getMeshEntryVolume( 0 );
     unsigned int totalNumEntries = numEntries_;
     unsigned int localNumEntries = totalNumEntries;
     unsigned int startEntry = 0;
     vector< unsigned int > localIndices( localNumEntries ); // empty
     for ( unsigned int i = 0; i < localNumEntries; ++i )
         localIndices[i] = i;
     vector< double > vols( localNumEntries, volume_ / numEntries_ );
     vector< vector< unsigned int > > outgoingEntries; // [node#][Entry#]
     vector< vector< unsigned int > > incomingEntries; // [node#][Entry#]
 
     // This function updates the size of the FieldDataHandler for the
     // MeshEntries.
     DataHandler* dh = meshEntry.element()->dataHandler();
     FieldDataHandlerBase* fdh = dynamic_cast< FieldDataHandlerBase* >( dh );
     assert( fdh );
     if ( totalNumEntries > fdh->getMaxFieldEntries() ) {
         fdh->setMaxFieldEntries( localNumEntries );
     }
 
     // This message tells the Stoich about the new mesh, and also about
     // how it communicates with other nodes.
     meshSplit()->fastSend( e,
         oldvol,
         vols, localIndices,
         outgoingEntries, incomingEntries );
 
     // This func goes down to the MeshEntry to tell all the pools and
     // Reacs to deal with the new mesh. They then update the stoich.
     lookupEntry( 0 )->triggerRemesh( meshEntry.eref(),
         oldvol, startEntry, localIndices, vols );
         */
 }

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void CylMesh::updateCoords	(	const Eref &	e,
		const vector< double > &	concs
	)

Recomputes all local coordinate and meshing data following a change in any of the coord parameters

This assumes that diffLength is the quantity to preserve, over numEntries. So when the compartment changes volume, numEntries changes. diffLength will be fine-tuned to be a clean multiple.

Definition at line 205 of file CylMesh.cpp.

References buildStencil(), diffLength_, doubleEq(), lenSlope_, numEntries_, r0_, r1_, rSlope_, ChemCompt::setChildConcs(), totLen_, x0_, x1_, y0_, y1_, z0_, and z1_.

Referenced by innerSetCoords(), setDiffLength(), setR0(), setR1(), setX0(), setX1(), setY0(), setY1(), setZ0(), and setZ1().

 {
     double temp = sqrt(
         ( x1_ - x0_ ) * ( x1_ - x0_ ) +
         ( y1_ - y0_ ) * ( y1_ - y0_ ) +
         ( z1_ - z0_ ) * ( z1_ - z0_ )
     );
 
     if ( doubleEq( temp, 0.0 ) ) {
         cout << "Error: CylMesh::updateCoords:\n"
         "total length of compartment = 0 with these parameters\n";
         return;
     }
     totLen_ = temp;
 
 
     temp = totLen_ / diffLength_;
     if ( temp < 1.0 ) {
         diffLength_ = totLen_;
         numEntries_ = 1;
     } else {
         numEntries_ = static_cast< unsigned int >( round ( temp ) );
         diffLength_ = totLen_ / numEntries_;
     }
     rSlope_ = ( r1_ - r0_ ) / numEntries_;
     lenSlope_ = diffLength_ * rSlope_ * 2 / ( r0_ + r1_ );
 
     // dx2_[0] = diffLength_;
     // dx2_[1] = diffLength_;
     buildStencil();
     setChildConcs( e, concs, 0 );
 }

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double CylMesh::vGetEntireVolume ( ) const

virtual

Inherited virtual. Returns entire volume of compartment.

Implements ChemCompt.

Definition at line 714 of file CylMesh.cpp.

References getMeshEntryVolume(), and numEntries_.

Referenced by innerHandleRequestMeshStats(), and vSetVolumeNotRates().

 {
     double vol = 0.0;
     for ( unsigned int i = 0; i < numEntries_; ++i )
         vol += getMeshEntryVolume( i );
     return vol;
 }

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const vector< double > & CylMesh::vGetVoxelMidpoint ( ) const

virtual

Virtual func so that derived classes can return voxel midpoint.

Implements ChemCompt.

Definition at line 676 of file CylMesh.cpp.

References numEntries_, x0_, x1_, y0_, y1_, z0_, and z1_.

 {
     static vector< double > midpoint( numEntries_ * 3, 0.0 );
     midpoint.resize( numEntries_ * 3 );
     double dx = ( x1_ - x0_ ) / numEntries_;
     double dy = ( y1_ - y0_ ) / numEntries_;
     double dz = ( z1_ - z0_ ) / numEntries_;
     vector< double >::iterator j = midpoint.begin();
     for ( unsigned int i = 0; i < numEntries_; ++i )
         *j++ = x0_ + dx * i;
     for ( unsigned int i = 0; i < numEntries_; ++i )
         *j++ = y0_ + dy * i;
     for ( unsigned int i = 0; i < numEntries_; ++i )
         *j++ = z0_ + dz * i;
 
     return midpoint;
 }

const vector< double > & CylMesh::vGetVoxelVolume ( ) const

virtual

Virtual func so that derived classes can pass voxel volume back.

Implements ChemCompt.

Definition at line 667 of file CylMesh.cpp.

References getMeshEntryVolume(), and numEntries_.

 {
     static vector< double > vol;
     vol.resize( numEntries_ );
     for ( unsigned int i = 0; i < numEntries_; ++i )
         vol[i] = getMeshEntryVolume( i );
     return vol;
 }

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bool CylMesh::vSetVolumeNotRates ( double volume )

virtual

Inherited virtual. Resizes len and dia of each voxel.

Implements ChemCompt.

Definition at line 722 of file CylMesh.cpp.

References diffLength_, numEntries_, r0_, r1_, totLen_, vGetEntireVolume(), x1_, y1_, and z1_.

 {
     double oldVol = vGetEntireVolume();
     double linScale = pow( volume/oldVol, 1.0 / 3.0 );
     x1_ *= linScale;
     y1_ *= linScale;
     z1_ *= linScale;
     r0_ *= linScale;
     r1_ *= linScale;
     totLen_ *= linScale;
     // Have to scale this so numEntries remains the same.
     diffLength_ = totLen_ / numEntries_;
     return true;
 }

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Member Data Documentation

double CylMesh::diffLength_

private

Radius at other end.

Definition at line 178 of file CylMesh.h.

Referenced by buildStencil(), getCoordinates(), getCoords(), getDiffLength(), innerSetCoords(), innerSetNumEntries(), matchCubeMeshEntries(), matchCylMeshEntries(), selectGridVolume(), setDiffLength(), updateCoords(), and vSetVolumeNotRates().

bool CylMesh::isToroid_

private

Definition at line 165 of file CylMesh.h.

Referenced by buildStencil(), getDiffusionArea(), getDiffusionScaling(), and getMeshType().

double CylMesh::lenSlope_

private

Utility value: dr/dx.

Definition at line 189 of file CylMesh.h.

Referenced by getCoordinates(), innerSetNumEntries(), and updateCoords().

unsigned int CylMesh::numEntries_

private

double CylMesh::r0_

private

coords

Definition at line 175 of file CylMesh.h.

Referenced by buildStencil(), getCoordinates(), getCoords(), getDiffusionArea(), getR0(), getVoxelArea(), innerSetCoords(), innerSetNumEntries(), matchCubeMeshEntries(), matchCylMeshEntries(), nearest(), selectGridVolume(), setR0(), updateCoords(), and vSetVolumeNotRates().

double CylMesh::r1_

private

Radius at one end.

Definition at line 176 of file CylMesh.h.

Referenced by buildStencil(), getCoordinates(), getCoords(), getR1(), getVoxelArea(), innerSetCoords(), innerSetNumEntries(), matchCylMeshEntries(), selectGridVolume(), setR1(), updateCoords(), and vSetVolumeNotRates().

double CylMesh::rSlope_

private

Utility value: Total length of cylinder.

Definition at line 188 of file CylMesh.h.

Referenced by buildStencil(), getCoordinates(), getDiffusionArea(), innerSetNumEntries(), matchCubeMeshEntries(), nearest(), and updateCoords().

double CylMesh::surfaceGranularity_

private

Length constant for diffusion. Equal to dx.

surfaceGranularity_ decides how finely to subdivide DiffLength or cubic mesh side, when computing surface area of intersections between them when diffusing. Defaults to 0.1

Definition at line 185 of file CylMesh.h.

Referenced by selectGridVolume().

double CylMesh::totLen_

private

Definition at line 187 of file CylMesh.h.

Referenced by getCoordinates(), getTotLength(), getVoxelLength(), innerSetNumEntries(), matchCubeMeshEntries(), matchCylMeshEntries(), updateCoords(), and vSetVolumeNotRates().