EndoMesh Class Reference

#include <EndoMesh.h>

Inheritance diagram for EndoMesh:

Collaboration diagram for EndoMesh:

Public Member Functions
	EndoMesh ()
double	extendedMeshEntryVolume (unsigned int fid) const
	Volume of mesh Entry including abutting diff-coupled voxels. More...
double	getApower (const Eref &e) const
double	getAscale (const Eref &e) const
vector< double >	getCoordinates (unsigned int fid) const
	Virtual function to return coords of mesh Entry. More...
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...
bool	getDoAxialDiffusion (const Eref &e) const
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	getRpower (const Eref &e) const
double	getRscale (const Eref &e) const
ObjId	getSurround (const Eref &e) const
const vector< double > &	getVoxelArea () const
const vector< double > &	getVoxelLength () const
double	getVpower (const Eref &e) const
double	getVscale (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
	Virtual function to return # of spatial dimensions of mesh. More...
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	innerSetNumEntries (unsigned int n)
	Inherited virtual func. More...
void	matchMeshEntries (const ChemCompt *other, vector< VoxelJunction > &ret) const
double	nearest (double x, double y, double z, unsigned int &index) const
void	setApower (const Eref &e, double v)
void	setAscale (const Eref &e, double v)
void	setDoAxialDiffusion (const Eref &e, bool v)
void	setRpower (const Eref &e, double v)
void	setRscale (const Eref &e, double v)
void	setSurround (const Eref &e, ObjId v)
void	setVpower (const Eref &e, double v)
void	setVscale (const Eref &e, double v)
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...
	~EndoMesh ()
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	aPower_
	rEndo = rScale * pow( surroundVol, rPower_) More...
double	aScale_
	aEndo = aScale * pow( surroundVol, aPower_) More...
bool	doAxialDiffusion_
	vEndo = vScale * pow( surroundVol, vPower_) More...
Id	insideMeshes_
const MeshCompt *	parent_
double	rPower_
	EndoMeshes inside. Used to update. More...
double	rScale_
	rEndo = rScale * pow( surroundVol, rPower_) More...
ObjId	surround_
double	vPower_
	aEndo = aScale * pow( surroundVol, aPower_) More...
double	vScale_
	vEndo = vScale * pow( surroundVol, vPower_) More...

Detailed Description

The EndoMesh is a cellular compartment entirely contained within another compartment. It supports diffusion only with its immediate surround, of which there can only be one, and with its immediate interior, which can be one or more EndoMeshes. Each voxel in the EndoMesh is well mixed, and does not exchange with any other voxels. Typically used in modelling endosomes, ER, mitochondria, and other organelles.

Definition at line 23 of file EndoMesh.h.

Constructor & Destructor Documentation

EndoMesh::EndoMesh

(

)

Definition at line 138 of file EndoMesh.cpp.

    :
        parent_( 0 ),
        rPower_( 1.0 / 3.0 ),
        rScale_( 0.5 ),
        aPower_( 0.5 ),
        aScale_( 0.25 ),
        vPower_( 1.0 ),
        vScale_( 0.125 ),
        doAxialDiffusion_( false )
{
    ;
}

EndoMesh::~EndoMesh

(

)

Definition at line 152 of file EndoMesh.cpp.

{
    ;
}

Member Function Documentation

double EndoMesh::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 307 of file EndoMesh.cpp.

References MeshCompt::extendedMeshEntryVolume(), parent_, vPower_, and vScale_.

{
    double vpa = parent_->extendedMeshEntryVolume( fid );
    return vScale_ * pow( vpa, vPower_ );
}

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double EndoMesh::getApower

(

const Eref &

e

)

const

Definition at line 186 of file EndoMesh.cpp.

References aPower_.

Referenced by initCinfo().

{
    return aPower_;
}

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double EndoMesh::getAscale

(

const Eref &

e

)

const

Definition at line 196 of file EndoMesh.cpp.

References aScale_.

Referenced by initCinfo().

{
    return aScale_;
}

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vector< double > EndoMesh::getCoordinates ( unsigned int  fid ) const

virtual

Virtual function to return coords of mesh Entry.

Virtual function to return coords of mesh Entry. For Endo mesh, coords are just middle of parent.

Implements ChemCompt.

Definition at line 277 of file EndoMesh.cpp.

References ChemCompt::getCoordinates(), and parent_.

{
    vector< double > temp = parent_->getCoordinates( fid );
    vector< double > ret;
    if ( temp.size() > 6 ) {
        ret.resize( 4 );
        ret[0] = 0.5 * (temp[0] + temp[3] );
        ret[1] = 0.5 * (temp[1] + temp[4] );
        ret[2] = 0.5 * (temp[2] + temp[5] );
        ret[3] = 0;
    }
    return ret;
}

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vector< double > EndoMesh::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 This applies if we have endo mesh voxels diffusing with each other

Implements ChemCompt.

Definition at line 293 of file EndoMesh.cpp.

References ChemCompt::getNumEntries(), and parent_.

{
    return vector< double >( parent_->getNumEntries(), 0.0 );
}

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

virtual

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

Virtual function to return scale factor for diffusion. 1 here. This applies if we have endo mesh voxels diffusing with each other

Implements ChemCompt.

Definition at line 300 of file EndoMesh.cpp.

References ChemCompt::getNumEntries(), and parent_.

{
    return vector< double >( parent_->getNumEntries(), 0.0 );
}

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bool EndoMesh::getDoAxialDiffusion

(

const Eref &

e

)

const

Definition at line 242 of file EndoMesh.cpp.

References doAxialDiffusion_.

Referenced by initCinfo().

{
    return doAxialDiffusion_;
}

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

virtual

Virtual function to return dimensions of specified entry.

Implements ChemCompt.

Definition at line 258 of file EndoMesh.cpp.

{
    return 3;
}

double EndoMesh::getMeshEntryVolume ( unsigned int  fid ) const

virtual

Virtual function to return volume of mesh Entry.

Implements ChemCompt.

Definition at line 269 of file EndoMesh.cpp.

References ChemCompt::getMeshEntryVolume(), parent_, vPower_, and vScale_.

{
    double vpa = parent_->getMeshEntryVolume( fid );
    return vScale_ * pow( vpa, vPower_ );
}

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

virtual

Virtual function to return MeshType of specified entry.

Implements ChemCompt.

Definition at line 252 of file EndoMesh.cpp.

References ENDO.

{
    return ENDO;
}

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

virtual

Inherited virtual, do nothing for now.

This means the sibling voxel immediately adjacent to it, not the voxel surrounding it. Should we wish to do diffusion we would need to use the parent voxel of the surround voxel. Otherewise use EMTPY_VOXEL == -1U.

Implements MeshCompt.

Definition at line 361 of file EndoMesh.cpp.

References doAxialDiffusion_, MeshCompt::getParentVoxel(), ChemCompt::innerGetNumEntries(), and parent_.

{
    if ( doAxialDiffusion_ )
        return parent_->getParentVoxel();

    vector< unsigned int > ret( parent_->innerGetNumEntries(), -1U );
    return ret;
}

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double EndoMesh::getRpower

(

const Eref &

e

)

const

Definition at line 166 of file EndoMesh.cpp.

References rPower_.

Referenced by initCinfo().

{
    return rPower_;
}

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double EndoMesh::getRscale

(

const Eref &

e

)

const

Definition at line 176 of file EndoMesh.cpp.

References rScale_.

Referenced by initCinfo().

{
    return rScale_;
}

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ObjId EndoMesh::getSurround

(

const Eref &

e

)

const

Definition at line 232 of file EndoMesh.cpp.

References surround_.

Referenced by initCinfo().

{
    return surround_;
}

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

virtual

Implements MeshCompt.

Definition at line 384 of file EndoMesh.cpp.

References aPower_, aScale_, parent_, and ChemCompt::vGetVoxelVolume().

Referenced by matchMeshEntries().

{
    static vector< double > ret;
    ret = parent_->vGetVoxelVolume();
    for ( auto i = ret.begin(); i != ret.end(); ++i )
        *i = aScale_ * pow( *i, aPower_ );
    return ret;
}

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

virtual

Implements MeshCompt.

Definition at line 393 of file EndoMesh.cpp.

References parent_, ChemCompt::vGetVoxelVolume(), vPower_, and vScale_.

{
    static vector< double > ret;
    ret = parent_->vGetVoxelVolume();
    for ( auto i = ret.begin(); i != ret.end(); ++i )
        *i = vScale_ * pow( *i, vPower_ );
    return ret;
}

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double EndoMesh::getVpower

(

const Eref &

e

)

const

Definition at line 206 of file EndoMesh.cpp.

References vPower_.

Referenced by initCinfo().

{
    return vPower_;
}

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double EndoMesh::getVscale

(

const Eref &

e

)

const

Definition at line 216 of file EndoMesh.cpp.

References vScale_.

Referenced by initCinfo().

{
    return vScale_;
}

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void EndoMesh::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 460 of file EndoMesh.cpp.

References ChemCompt::indexToSpace(), and parent_.

{
    parent_->indexToSpace( index, x, y, z );
}

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const Cinfo * EndoMesh::initCinfo ( )

static

Definition at line 26 of file EndoMesh.cpp.

References endoMeshCinfo, getApower(), getAscale(), getDoAxialDiffusion(), getRpower(), getRscale(), getSurround(), getVpower(), getVscale(), ChemCompt::initCinfo(), setApower(), setAscale(), setDoAxialDiffusion(), setRpower(), setRscale(), setSurround(), setVpower(), and setVscale().

{
        // Field Definitions
        static ElementValueFinfo< EndoMesh, double > rPower(
            "rPower",
            "Used in rEndo = rScale * pow(surroundVol, rPower)."
            "Used to obtain radius of each endo voxel from matching "
            "surround voxel. Defaults to 1/3",
            &EndoMesh::setRpower,
            &EndoMesh::getRpower
        );
        static ElementValueFinfo< EndoMesh, double > rScale(
            "rScale",
            "Used in rEndo = rScale * pow(surroundVol, rPower)."
            "Used to obtain radius of each endo voxel from matching "
            "surround voxel. Defaults to 0.5",
            &EndoMesh::setRscale,
            &EndoMesh::getRscale
        );
        static ElementValueFinfo< EndoMesh, double > aPower(
            "aPower",
            "Used in rEndo = aScale * pow(surroundVol, aPower)."
            "Used to obtain area of each endo voxel from matching "
            "surround voxel. Defaults to 1/2",
            &EndoMesh::setApower,
            &EndoMesh::getApower
        );
        static ElementValueFinfo< EndoMesh, double > aScale(
            "aScale",
            "Used in rEndo = aScale * pow(surroundVol, aPower)."
            "Used to obtain area of each endo voxel from matching "
            "surround voxel. Defaults to 0.25",
            &EndoMesh::setAscale,
            &EndoMesh::getAscale
        );
        static ElementValueFinfo< EndoMesh, double > vPower(
            "vPower",
            "Used in rEndo = vScale * pow(surroundVol, vPower)."
            "Used to obtain volume of each endo voxel from matching "
            "surround voxel. Defaults to 1.",
            &EndoMesh::setVpower,
            &EndoMesh::getVpower
        );
        static ElementValueFinfo< EndoMesh, double > vScale(
            "vScale",
            "Used in rEndo = vScale * pow(surroundVol, vPower)."
            "Used to obtain volume of each endo voxel from matching "
            "surround voxel. Defaults to 0.125",
            &EndoMesh::setVscale,
            &EndoMesh::getVscale
        );

        static ElementValueFinfo< EndoMesh, ObjId > surround(
            "surround",
            "ObjId of compartment surrounding current EndoMesh",
            &EndoMesh::setSurround,
            &EndoMesh::getSurround
        );

        static ElementValueFinfo< EndoMesh, bool > doAxialDiffusion(
            "doAxialDiffusion",
            "Flag to determine if endoMesh should undertake axial "
            "diffusion. Defaults to 'false'. "
            "Should only be used within NeuroMesh and CylMesh. "
            "Must be assigned before Dsolver is built.",
            &EndoMesh::setDoAxialDiffusion,
            &EndoMesh::getDoAxialDiffusion
        );


        // MsgDest Definitions

        // Field Elements

    static Finfo* endoMeshFinfos[] = {
        &rPower,            // Value
        &rScale,            // Value
        &aPower,            // Value
        &aScale,            // Value
        &vPower,            // Value
        &vScale,            // Value
        &surround,          // Value
        &doAxialDiffusion,  // Value
    };

    static Dinfo< EndoMesh > dinfo;
    static Cinfo endoMeshCinfo (
        "EndoMesh",
        ChemCompt::initCinfo(),
        endoMeshFinfos,
        sizeof( endoMeshFinfos ) / sizeof ( Finfo* ),
        &dinfo
    );

    return &endoMeshCinfo;
}

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void EndoMesh::innerBuildDefaultMesh ( const Eref &  e, double  volume, unsigned int  numEntries  )

virtual

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

Implements ChemCompt.

Definition at line 350 of file EndoMesh.cpp.

{
}

unsigned int EndoMesh::innerGetDimensions ( ) const

virtual

Virtual function to return # of spatial dimensions of mesh.

Implements ChemCompt.

Definition at line 264 of file EndoMesh.cpp.

{
    return 1;
}

unsigned int EndoMesh::innerGetNumEntries ( ) const

virtual

Inherited virtual func. Returns number of MeshEntry in array

Implements ChemCompt.

Definition at line 336 of file EndoMesh.cpp.

References ChemCompt::innerGetNumEntries(), and parent_.

{
    return parent_->innerGetNumEntries();
}

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

virtual

Implements ChemCompt.

Definition at line 326 of file EndoMesh.cpp.

{
}

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

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

Definition at line 318 of file EndoMesh.cpp.

References ChemCompt::getNumEntries(), parent_, and vGetEntireVolume().

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

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void EndoMesh::innerSetNumEntries ( unsigned int  n )

virtual

Inherited virtual func.

Inherited virtual func. Dummy, because the EndoMesh just does what its parent does.

Implements ChemCompt.

Definition at line 345 of file EndoMesh.cpp.

{
}

void EndoMesh::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.

Consider concentric EndoMeshes in an outer cyl/sphere of radius r_0. Radii, from out to in, are r_0, r_1, r_2.... r_innermost. Consider that we are on EndoMesh n. The diffusion length in each case is 1/2(r_n-1 - r_n+1). For the innermost we use r_n+1 = 0 The diffusion XA is the area of the EndoMesh.

Implements ChemCompt.

Definition at line 420 of file EndoMesh.cpp.

References getVoxelArea(), MeshCompt::getVoxelLength(), PI, vGetVoxelVolume(), and ChemCompt::vGetVoxelVolume().

Referenced by CylMesh::matchMeshEntries(), CubeMesh::matchMeshEntries(), and NeuroMesh::matchMeshEntries().

{
    vector< double > vol = other->vGetVoxelVolume();
    const MeshCompt* mc = static_cast< const MeshCompt* >( other );
    vector< double > len = mc->getVoxelLength();
    assert( vol.size() == len.size() );
    ret.resize( vol.size() );
    vector< double > myVol = vGetVoxelVolume();
    assert( myVol.size() == vol.size() );
    vector< double > myArea = getVoxelArea();
    assert( myArea.size() == vol.size() );

    for ( unsigned int i = 0; i < vol.size(); ++i ) {
        double rSurround = sqrt( vol[i] / (len[i] * PI ) );
        ret[i].first = ret[i].second = i;
        ret[i].firstVol = myVol[i];
        ret[i].secondVol = vol[i];

        // For now we don't consider internal EndoMeshes.
        ret[i].diffScale = 2.0 * myArea[i] / rSurround;
    }
}

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double EndoMesh::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 453 of file EndoMesh.cpp.

References ChemCompt::nearest(), and parent_.

{
    return parent_->nearest( x, y, z, index );
}

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void EndoMesh::setApower	(	const Eref &	e,
		double	v
	)

Definition at line 181 of file EndoMesh.cpp.

References aPower_.

Referenced by initCinfo().

{
    aPower_ = v;
}

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void EndoMesh::setAscale	(	const Eref &	e,
		double	v
	)

Definition at line 191 of file EndoMesh.cpp.

References aScale_.

Referenced by initCinfo().

{
    aScale_ = v;
}

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void EndoMesh::setDoAxialDiffusion	(	const Eref &	e,
		bool	v
	)

Definition at line 237 of file EndoMesh.cpp.

References doAxialDiffusion_.

Referenced by initCinfo().

{
    doAxialDiffusion_ = v;
}

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void EndoMesh::setRpower	(	const Eref &	e,
		double	v
	)

Definition at line 161 of file EndoMesh.cpp.

References rPower_.

Referenced by initCinfo().

{
    rPower_ = v;
}

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void EndoMesh::setRscale	(	const Eref &	e,
		double	v
	)

Definition at line 171 of file EndoMesh.cpp.

References rScale_.

Referenced by initCinfo().

{
    rScale_ = v;
}

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void EndoMesh::setSurround	(	const Eref &	e,
		ObjId	v
	)

Definition at line 221 of file EndoMesh.cpp.

References Element::cinfo(), ObjId::data(), ObjId::element(), Cinfo::isA(), Cinfo::name(), parent_, ObjId::path(), and surround_.

Referenced by initCinfo().

{
    if ( !v.element()->cinfo()->isA( "ChemCompt" ) ) {
        cout << "Warning: 'surround' may only be set to an object of class 'ChemCompt'\n";
        cout << v.path() << " is of class " << v.element()->cinfo()->name() << endl;
        return;
    }
    surround_ = v;
    parent_ = reinterpret_cast< const MeshCompt* >( v.data() );
}

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void EndoMesh::setVpower	(	const Eref &	e,
		double	v
	)

Definition at line 201 of file EndoMesh.cpp.

References vPower_.

Referenced by initCinfo().

{
    vPower_ = v;
}

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void EndoMesh::setVscale	(	const Eref &	e,
		double	v
	)

Definition at line 211 of file EndoMesh.cpp.

References vScale_.

Referenced by initCinfo().

{
    vScale_ = v;
}

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double EndoMesh::vGetEntireVolume ( ) const

virtual

Inherited virtual. Returns entire volume of compartment.

Implements ChemCompt.

Definition at line 402 of file EndoMesh.cpp.

References vGetVoxelVolume().

Referenced by innerHandleRequestMeshStats().

{
    double vol = 0.0;
    auto vec = vGetVoxelVolume();
    for ( auto i = vec.begin(); i != vec.end(); ++i )
        vol += *i;
    return vol;
}

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

virtual

Virtual func so that derived classes can return voxel midpoint.

Implements ChemCompt.

Definition at line 379 of file EndoMesh.cpp.

References parent_, and ChemCompt::vGetVoxelMidpoint().

{
    return parent_->vGetVoxelMidpoint();
}

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

virtual

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

Implements ChemCompt.

Definition at line 370 of file EndoMesh.cpp.

References parent_, ChemCompt::vGetVoxelVolume(), vPower_, and vScale_.

Referenced by matchMeshEntries(), and vGetEntireVolume().

{
    static vector< double > ret;
    ret = parent_->vGetVoxelVolume();
    for ( auto i = ret.begin(); i != ret.end(); ++i )
        *i = vScale_ * pow( *i, vPower_ );
    return ret;
}

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bool EndoMesh::vSetVolumeNotRates ( double  volume )

virtual

Inherited virtual. Resizes len and dia of each voxel.

Implements ChemCompt.

Definition at line 411 of file EndoMesh.cpp.

{
    return true; // maybe should be false? Unsure
}

Member Data Documentation

double EndoMesh::aPower_

private

rEndo = rScale * pow( surroundVol, rPower_)

Definition at line 142 of file EndoMesh.h.

Referenced by getApower(), getVoxelArea(), and setApower().

double EndoMesh::aScale_

private

aEndo = aScale * pow( surroundVol, aPower_)

Definition at line 143 of file EndoMesh.h.

Referenced by getAscale(), getVoxelArea(), and setAscale().

bool EndoMesh::doAxialDiffusion_

private

vEndo = vScale * pow( surroundVol, vPower_)

Definition at line 147 of file EndoMesh.h.

Referenced by getDoAxialDiffusion(), getParentVoxel(), and setDoAxialDiffusion().

Id EndoMesh::insideMeshes_

private

Definition at line 133 of file EndoMesh.h.

const MeshCompt* EndoMesh::parent_

private

Definition at line 131 of file EndoMesh.h.

Referenced by extendedMeshEntryVolume(), getCoordinates(), getDiffusionArea(), getDiffusionScaling(), getMeshEntryVolume(), getParentVoxel(), getVoxelArea(), getVoxelLength(), indexToSpace(), innerGetNumEntries(), innerHandleRequestMeshStats(), nearest(), setSurround(), vGetVoxelMidpoint(), and vGetVoxelVolume().

double EndoMesh::rPower_

private

EndoMeshes inside. Used to update.

The reason why the powers don't have to be 1/3, 1/2 and 1 is because some organelles are not a simple linear vol relationship with their surround. I want to keep flexibility.

Definition at line 140 of file EndoMesh.h.

Referenced by getRpower(), and setRpower().

double EndoMesh::rScale_

private

rEndo = rScale * pow( surroundVol, rPower_)

Definition at line 141 of file EndoMesh.h.

Referenced by getRscale(), and setRscale().

ObjId EndoMesh::surround_

private

Surrounding mesh. Use this for calculating all volume and diffusion terms, don't maintain any local variables.

Definition at line 130 of file EndoMesh.h.

Referenced by getSurround(), and setSurround().

double EndoMesh::vPower_

private

aEndo = aScale * pow( surroundVol, aPower_)

Definition at line 144 of file EndoMesh.h.

Referenced by extendedMeshEntryVolume(), getMeshEntryVolume(), getVoxelLength(), getVpower(), setVpower(), and vGetVoxelVolume().

double EndoMesh::vScale_

private

vEndo = vScale * pow( surroundVol, vPower_)

Definition at line 145 of file EndoMesh.h.

Referenced by extendedMeshEntryVolume(), getMeshEntryVolume(), getVoxelLength(), getVscale(), setVscale(), and vGetVoxelVolume().

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

• moose-core/mesh/EndoMesh.h
• moose-core/mesh/EndoMesh.cpp