#include <CubeMesh.h>

Inheritance diagram for CubeMesh:

Collaboration diagram for CubeMesh:

Public Member Functions
void	addStoich (Id stoich)

void	assignVoxels (vector< pair< unsigned int, unsigned int > > &intersect, double xmin, double xmax, double ymin, double ymax, double zmin, double zmax) const

void	buildMesh (Id geom, double x, double y, double z)

void	buildStencil ()

int	compareMeshSpacing (const CubeMesh *other) const
	Return 0 if spacing same, -1 if self smaller, +1 if self bigger. More...

	CubeMesh ()

void	defineIntersection (const CubeMesh *other, double &xmin, double &xmax, double &ymin, double &ymax, double &zmin, double &zmax) const
	Defines a cuboid volume of intersection between self and other. More...

void	deriveM2sFromS2m ()

void	deriveS2mFromM2s ()

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

void	fillSpaceToMeshLookup ()

void	fillThreeDimSurface ()

void	fillTwoDimSurface ()
	Fills surface_ vector with spatial meshIndices for a rectangle. More...

bool	getAlwaysDiffuse () const

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

vector< double >	getCoords (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...

double	getDx () const

double	getDy () const

double	getDz () const

bool	getIsToroid () 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...

vector< unsigned int >	getMeshToSpace () const

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

unsigned int	getNx () const

unsigned int	getNy () const

unsigned int	getNz () const

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

bool	getPreserveNumEntries () const

vector< unsigned int >	getSpaceToMesh () const

vector< unsigned int >	getSurface () const

const vector< double > &	getVoxelArea () const

const vector< double > &	getVoxelLength () const

double	getX0 () const

double	getX1 () const

double	getY0 () const

double	getY1 () const

double	getZ0 () const

double	getZ1 () const

void	indexToSpace (unsigned int index, double &x, double &y, double &z) const
	Converts the integer meshIndex to spatial coords. More...

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 vector< double > &v)

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

bool	isInsideCuboid (double x, double y, double z) const

bool	isInsideSpheroid (double x, double y, double z) const

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

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

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

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

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

unsigned int	neighbor (unsigned int spaceIndex, int dx, int dy, int dz) const

unsigned int	numDims () const
	Utility function for returning # of dimensions in mesh. More...

void	setAlwaysDiffuse (bool v)

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

void	setDiffScale (const CubeMesh *other, vector< VoxelJunction > &ret) const
	Assigns diffusion scaling info for the voxel junctions. More...

void	setDx (double v)

void	setDy (double v)

void	setDz (double v)

void	setIsToroid (bool v)

void	setJunctionVol (const CubeMesh *other, vector< VoxelJunction > &ret) const
	Assigns volume info for the voxel junctions. More...

void	setMeshToSpace (vector< unsigned int > v)

void	setNx (unsigned int v)

void	setNy (unsigned int v)

void	setNz (unsigned int v)

void	setPreserveNumEntries (bool v)

void	setSpaceToMesh (vector< unsigned int > v)

void	setSurface (vector< unsigned int > v)

void	setX0 (double v)

void	setX1 (double v)

void	setY0 (double v)

void	setY1 (double v)

void	setZ0 (double v)

void	setZ1 (double v)

unsigned int	spaceToIndex (double x, double y, double z) const
	Converts the 3-D coords to an index. EMPTY if out of range. More...

const vector< unsigned int > &	surface () const
	Utility and test function to read surface. More...

void	transmitChange (const Eref &e, double oldvol)

void	updateCoords ()

void	updateM2s ()

void	updateS2m ()

double	vGetEntireVolume () const
	Virtual func to get volume of entire 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)
	Virtual func, assigns volume, usually to single voxel. More...

	~CubeMesh ()

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 ()

Static Public Attributes
static const unsigned int	ABUTX = ~2

static const unsigned int	ABUTY = ~3

static const unsigned int	ABUTZ = ~4

static const unsigned int	EMPTY = ~0

static const unsigned int	MULTI = ~5

static const unsigned int	SURFACE = ~1

Private Attributes
bool	alwaysDiffuse_
	Flag: Should dx change or nx, with vol? More...

double	dx_
	coords More...

double	dy_
	Cuboid edge. More...

double	dz_
	Cuboid edge. More...

bool	isToroid_

vector< unsigned int >	m2s_
	of entries in z in surround volume More...

unsigned int	nx_
	Cuboid edge. More...

unsigned int	ny_
	of entries in x in surround volume More...

unsigned int	nz_
	of entries in y in surround volume More...

bool	preserveNumEntries_
	Flag: Should the ends loop around mathemagically? More...

vector< unsigned int >	s2m_

vector< unsigned int >	surface_

double	x0_
	Flag: should all voxels diffuse to any tgt? More...

double	x1_
	coords More...

double	y0_
	coords More...

double	y1_
	coords More...

double	z0_
	coords More...

double	z1_
	coords More...

Detailed Description

The CubeMesh represents a chemically identified compartment shaped like a cuboid. This is not really an effective geometry for most neurons because it would have to be rather finely subdivided to fit a typical dendrite or soma volume, but it is general.

Definition at line 19 of file CubeMesh.h.

Constructor & Destructor Documentation

CubeMesh::CubeMesh ( )

Definition at line 261 of file CubeMesh.cpp.

References updateCoords().

     :
         isToroid_( 0 ),
         preserveNumEntries_( 1 ),
         alwaysDiffuse_( false ),
         x0_( 0.0 ),
         y0_( 0.0 ),
         z0_( 0.0 ),
         x1_( 10e-6 ),
         y1_( 10e-6 ),
         z1_( 10e-6 ),
         dx_( 10e-6 ),
         dy_( 10e-6 ),
         dz_( 10e-6 ),
         nx_( 1 ),
         ny_( 1 ),
         nz_( 1 ),
         m2s_( 1, 0 ),
         s2m_( 1, 0 )
 {
     updateCoords();
 }

Here is the call graph for this function:

CubeMesh::~CubeMesh ( )

Definition at line 284 of file CubeMesh.cpp.

 {
     ;
 }

Member Function Documentation

void CubeMesh::addStoich ( Id stoich )

void CubeMesh::assignVoxels	(	vector< pair< unsigned int, unsigned int > > &	intersect,
		double	xmin,
		double	xmax,
		double	ymin,
		double	ymax,
		double	zmin,
		double	zmax
	)		const

Definition at line 1410 of file CubeMesh.cpp.

References dx_, dy_, dz_, indexToSpace(), nx_, ny_, nz_, s2m_, setIntersectVoxel(), surface_, x0_, y0_, and z0_.

Referenced by matchCubeMeshEntries().

 {
     unsigned int nx = 0.5 + ( xmax - xmin ) / dx_;
     unsigned int ny = 0.5 + ( ymax - ymin ) / dy_;
     unsigned int nz = 0.5 + ( zmax - zmin ) / dz_;
     // offset terms for nx, ny, nz from coord system for coarser grid.
     // Note that these can go negative if the intersect grid goes past
     // the coarse grid.
     int ox = round( ( xmin - x0_ ) / dx_ );
     int oy = round( ( ymin - y0_ ) / dy_ );
     int oz = round( ( zmin - z0_ ) / dz_ );
 
     // Scan through mesh surface using coarser grid, assign cuboid voxels
     for ( vector< unsigned int >::const_iterator i = surface_.begin();
                     i != surface_.end(); ++i ) {
         unsigned int index = *i;
         double x, y, z;
         indexToSpace( index, x, y, z );
         if ( x >= xmin && x <= xmax && y >= ymin && y <= ymax &&
                         z >= zmin && z <= zmax ) {
             int ix = index % nx_ - ox;
             assert( ix >= 0 );
             unsigned int uix = ix;
             index /= nx_;
             int iy = index % ny_ - oy;
             assert( iy >= 0 );
             unsigned int uiy = iy;
             index /= ny_;
             int iz = index % nz_ - oz;
             assert( iz >= 0 );
             unsigned int uiz = iz;
             unsigned int meshIndex = s2m_[ *i ];
 
             setIntersectVoxel( intersect, uix, uiy, uiz, nx, ny, nz,
                             meshIndex );
         }
     }
 }

Here is the call graph for this function:

Here is the caller graph for this function:

void CubeMesh::buildMesh	(	Id	geom,
		double	x,
		double	y,
		double	z
	)

Definition at line 697 of file CubeMesh.cpp.

Referenced by initCinfo().

 {
     ;
 }

Here is the caller graph for this function:

void CubeMesh::buildStencil ( )

Sets up the stencil that defines how to combine neighboring mesh elements to set up the diffusion du/dt term, using the method of lines. This is a very general function. It uses the information in the m2s_ and s2m_ vectors to work out the adjacency matrix. So we could use an arbitrary 3-D image to define the diffusive volume and boundaries using m2s_ and s2m_. We could also use geometric shapes through the fillSpaceToMeshLookup() function, which is currently a dummy and just does a cuboid.

Definition at line 1060 of file CubeMesh.cpp.

References MeshCompt::addRow(), dx_, dy_, dz_, EMPTY, MeshCompt::innerResetStencil(), m2s_, nx_, ny_, nz_, s2m_, and MeshCompt::setStencilSize().

Referenced by deriveM2sFromS2m(), deriveS2mFromM2s(), and updateCoords().

 {
     static const unsigned int flag = EMPTY;
 
 
     // fillSpaceToMeshLookup();
     unsigned int num = m2s_.size();
     setStencilSize( num, num );
     for ( unsigned int i = 0; i < num; ++i ) {
         unsigned int q = m2s_[i];
         unsigned int ix = q % nx_;
         unsigned int iy = ( q / nx_ ) % ny_;
         unsigned int iz = ( q / ( nx_ * ny_ ) ) % nz_;
         vector< double > entry;
         vector< unsigned int > colIndex;
         vector< Ecol > e;
 
         if ( ix > 0 && s2m_[q-1] != flag ) {
             e.push_back( Ecol( dy_ * dz_ / dx_, s2m_[q-1] ) );
         }
         if ( ( ix < nx_ - 1 ) && s2m_[q+1] != flag ) {
             e.push_back( Ecol( dy_ * dz_ / dx_, s2m_[q+1] ) );
         }
         if ( iy > 0 && s2m_[ q-nx_ ] != flag ) {
             assert( q >= nx_ );
             e.push_back( Ecol( dx_ * dz_ / dy_, s2m_[q-nx_] ) );
         }
         if ( iy < ny_ - 1 && s2m_[ q+nx_ ] != flag ) {
             assert( q+nx_ < s2m_.size() );
             e.push_back( Ecol( dx_ * dz_ / dy_, s2m_[q+nx_] ) );
         }
         if ( iz > 0 && s2m_[ q - nx_*ny_ ] != flag ) {
             assert( q >= nx_ * ny_ );
             e.push_back( Ecol( dx_ * dy_ / dz_, s2m_[q - nx_ * ny_] ) );
         }
         if ( iz < nz_ - 1 && s2m_[ q + nx_*ny_ ] ) {
             assert( q+nx_ < s2m_.size() );
             e.push_back( Ecol( dx_ * dy_ / dz_, s2m_[q + nx_ * ny_] ) );
         }
         sort( e.begin(), e.end() );
         for ( vector< Ecol >::iterator j = e.begin(); j != e.end(); ++j ) {
             entry.push_back( j->e_ );
             colIndex.push_back( j->col_ );
         }
         addRow( i, entry, colIndex );
     }
     innerResetStencil();
 }

Here is the call graph for this function:

Here is the caller graph for this function:

int CubeMesh::compareMeshSpacing ( const CubeMesh * other ) const

Return 0 if spacing same, -1 if self smaller, +1 if self bigger.

Definition at line 1222 of file CubeMesh.cpp.

References doubleApprox(), dx_, dy_, and dz_.

Referenced by matchCubeMeshEntries().

 {
     if ( doubleApprox( dx_, other->dx_ ) &&
         doubleApprox( dy_, other->dy_ ) &&
         doubleApprox( dz_, other->dz_ ) )
             return 0; // equal
 
     if ( dx_ >= other->dx_ &&
         dy_ >= other->dy_ &&
         dz_ >= other->dz_ )
         return 1; // bigger
 
     if ( dx_ <= other->dx_ &&
         dy_ <= other->dy_ &&
         dz_ <= other->dz_ )
         return -1; // smaller than other.
 
 
     cout << "Warning: CubeMesh::compareMeshSpacing: inconsistent spacing\n";
     return 0;
 }

Here is the call graph for this function:

Here is the caller graph for this function:

void CubeMesh::defineIntersection	(	const CubeMesh *	other,
		double &	xmin,
		double &	xmax,
		double &	ymin,
		double &	ymax,
		double &	zmin,
		double &	zmax
	)		const

Defines a cuboid volume of intersection between self and other.

Definition at line 1244 of file CubeMesh.cpp.

References dx_, dy_, dz_, swapIfBackward(), x0_, x1_, y0_, y1_, z0_, and z1_.

Referenced by matchCubeMeshEntries().

 {
     const double meshSlop = 0.2;
     xmin = ( x0_ > other->x0_ ) ? x0_ : other->x0_;
     xmax = ( x1_ < other->x1_ ) ? x1_ : other->x1_;
     ymin = ( y0_ > other->y0_ ) ? y0_ : other->y0_;
     ymax = ( y1_ < other->y1_ ) ? y1_ : other->y1_;
     zmin = ( z0_ > other->z0_ ) ? z0_ : other->z0_;
     zmax = ( z1_ < other->z1_ ) ? z1_ : other->z1_;
     // Align to coarser mesh
     double temp = ( xmin - x0_) / dx_;
     if ( temp - floor( temp ) > meshSlop )
         xmin = floor( temp ) * dx_;
     temp = ( ymin - y0_) / dy_;
     if ( temp - floor( temp ) > meshSlop )
         ymin = floor( temp ) * dy_;
     temp = ( zmin - z0_) / dz_;
     if ( temp - floor( temp ) > meshSlop )
         zmin = floor( temp ) * dz_;
 
     // Provide 1 voxel padding all around.
     xmin -= dx_;
     xmax += dx_;
     ymin -= dy_;
     ymax += dy_;
     zmin -= dz_;
     zmax += dz_;
     swapIfBackward( xmin, xmax );
     swapIfBackward( ymin, ymax );
     swapIfBackward( zmin, zmax );
 }

Here is the call graph for this function:

Here is the caller graph for this function:

void CubeMesh::deriveM2sFromS2m ( )

Updates the m2s_ vector after s2m_ has been changed, and rebuilds the Stencil too. Any earlier junction information is lost.

Definition at line 1033 of file CubeMesh.cpp.

References buildStencil(), EMPTY, m2s_, nx_, ny_, nz_, and s2m_.

Referenced by setSpaceToMesh().

 {
     m2s_.clear();
     assert( s2m_.size() == nx_ * ny_ * nz_ );
     for ( unsigned int i = 0; i < s2m_.size(); ++i ) {
         if ( s2m_[i] != EMPTY ) {
             m2s_.push_back( i );
             assert( m2s_.size() == s2m_[i] + 1 );
         }
     }
     buildStencil();
 }

Here is the call graph for this function:

Here is the caller graph for this function:

void CubeMesh::deriveS2mFromM2s ( )

Updates the s2m_ vector after m2s_ has been changed, and rebuilds the Stencil too. Any earlier junction information is lost.

Definition at line 1046 of file CubeMesh.cpp.

References buildStencil(), EMPTY, m2s_, nx_, ny_, nz_, and s2m_.

Referenced by setMeshToSpace().

 {
     s2m_.clear();
     s2m_.resize( nx_ * ny_ * nz_, EMPTY );
     for ( unsigned int i = 0; i < m2s_.size(); ++i ) {
         s2m_[ m2s_[i] ] = i;
     }
     buildStencil();
 }

Here is the call graph for this function:

Here is the caller graph for this function:

double CubeMesh::extendedMeshEntryVolume ( unsigned int fid ) const

virtual

Virtual function to return volume of mesh Entry, including.

Utility function to return volume of any voxel including those diffusively coupled and aubtting the present volume.

Implements ChemCompt.

Definition at line 791 of file CubeMesh.cpp.

References dx_, dy_, dz_, MeshCompt::extendedMeshEntryVolume(), and m2s_.

 {
     if ( fid >= m2s_.size() ) {
         return MeshCompt::extendedMeshEntryVolume( fid - m2s_.size() );
     }
     return dx_ * dy_ * dz_;
 }

Here is the call graph for this function:

void CubeMesh::fillSpaceToMeshLookup ( )

Definition at line 1005 of file CubeMesh.cpp.

References dx_, dy_, dz_, EMPTY, isInsideCuboid(), m2s_, nx_, ny_, nz_, s2m_, x0_, y0_, and z0_.

 {
     static const unsigned int flag = EMPTY;
     unsigned int num = 0;
     unsigned int q = 0;
     m2s_.clear();
     s2m_.resize( nx_ * ny_ * nz_, flag );
     for( unsigned int k = 0; k < nz_; ++k ) {
         double z = k * dz_ + z0_;
         for( unsigned int j = 0; j < ny_; ++j ) {
             double y = j * dy_ + y0_;
             for( unsigned int i = 0; i < nx_; ++i ) {
                 double x = i * dx_ + x0_;
                 if ( isInsideCuboid( x, y, z ) ) {
                     s2m_[q] = num;
                     m2s_.push_back( q );
                     ++num;
                 } else {
                     s2m_[q] = flag;
                 }
                 ++q;
             }
         }
     }
     assert( m2s_.size() == num );
 }

Here is the call graph for this function:

void CubeMesh::fillThreeDimSurface ( )

Fills surface_ vector with spatial meshIndices for a cuboid, that is, puts the surfaces of the cuboid in the vector.

Definition at line 340 of file CubeMesh.cpp.

References nx_, ny_, nz_, and surface_.

Referenced by updateCoords().

 {
     unsigned int size = nx_ * ny_ * nz_;
     // z == 0 plane
     for ( unsigned int j = 0; j < ny_; ++j )
         for ( unsigned int k = 0; k < nx_; ++k )
             surface_.push_back( j * nx_ + k );
     // z == nz_-1 plane
     unsigned int offset = size - nx_ * ny_;
     for ( unsigned int j = 0; j < ny_; ++j )
         for ( unsigned int k = 0; k < nx_; ++k )
             surface_.push_back( offset + j * nx_ + k );
 
     // y == 0 plane
     for ( unsigned int i = 0; i < nz_; ++i )
         for ( unsigned int k = 0; k < nx_; ++k )
             surface_.push_back( i * nx_ * ny_ + k );
     // y == ny_-1 plane
     offset = nx_ * ( ny_ - 1 );
     for ( unsigned int i = 0; i < nz_; ++i )
         for ( unsigned int k = 0; k < nx_; ++k )
             surface_.push_back( offset + i * nx_ * ny_ + k );
 
     // x == 0 plane
     for ( unsigned int i = 0; i < nz_; ++i )
         for ( unsigned int j = 0; j < ny_; ++j )
             surface_.push_back( ( i * ny_ + j ) * nx_ );
     // x == nx_-1 plane
     offset = nx_ - 1;
     for ( unsigned int i = 0; i < nz_; ++i )
         for ( unsigned int j = 0; j < ny_; ++j )
             surface_.push_back( offset + ( i * ny_ + j ) * nx_ );
 
     sort( surface_.begin(), surface_.end() );
     surface_.erase( unique( surface_.begin(), surface_.end() ),
                     surface_.end() );
 }

Here is the caller graph for this function:

void CubeMesh::fillTwoDimSurface ( )

Fills surface_ vector with spatial meshIndices for a rectangle.

Definition at line 303 of file CubeMesh.cpp.

References nx_, ny_, nz_, and surface_.

 {
     unsigned int size = nx_ * ny_ * nz_;
     if ( nx_ == 1 ) {
         for ( unsigned int j = 0; j < ny_; ++j )
             surface_.push_back( j  );
         for ( unsigned int j = size - ny_; j < size; ++j )
             surface_.push_back( j  );
         for ( unsigned int i = 1; i < nz_ - 1; ++i )
             surface_.push_back( i * ny_  );
         for ( unsigned int i = 1; i < nz_ - 1; ++i )
             surface_.push_back( ny_ - 1 + i * ny_  );
     } else if ( ny_ == 1 ) {
         for ( unsigned int k = 0; k < nx_; ++k )
             surface_.push_back( k  );
         for ( unsigned int k = size - nx_; k < size; ++k )
             surface_.push_back( k  );
         for ( unsigned int i = 1; i < nz_ - 1; ++i )
             surface_.push_back( i * nx_  );
         for ( unsigned int i = 1; i < nz_ - 1; ++i )
             surface_.push_back( nx_ - 1 + i * nx_  );
     } else if ( nz_ == 1 ) {
         for ( unsigned int k = 0; k < nx_; ++k )
             surface_.push_back( k  );
         for ( unsigned int k = size - nx_; k < size; ++k )
             surface_.push_back( k  );
         for ( unsigned int j = 1; j < ny_ - 1; ++j )
             surface_.push_back( j * nx_  );
         for ( unsigned int j = 1; j < ny_ - 1; ++j )
             surface_.push_back( j * nx_ + nx_ - 1  );
     }
     // Ah, C++ STL. Look on my works, ye mighty, and despair.
     sort( surface_.begin(), surface_.end() );
     surface_.erase( unique( surface_.begin(), surface_.end() ),
                     surface_.end() );
 }

bool CubeMesh::getAlwaysDiffuse ( ) const

Definition at line 596 of file CubeMesh.cpp.

References alwaysDiffuse_.

Referenced by initCinfo().

 {
     // alwaysDiffuse is normally false.
     return alwaysDiffuse_;
 }

Here is the caller graph for this function:

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

virtual

Virtual function to return coords of mesh Entry.

Virtual function to return coords of mesh Entry. For Cuboid mesh, coords are x1y1z1 x2y2z2

Implements ChemCompt.

Definition at line 801 of file CubeMesh.cpp.

References dx_, dy_, dz_, m2s_, nx_, ny_, nz_, x0_, y0_, and z0_.

 {
     assert( fid < m2s_.size() );
     unsigned int spaceIndex = m2s_[fid];
 
     unsigned int ix = spaceIndex % nx_;
     unsigned int iy = (spaceIndex / nx_) % ny_;
     unsigned int iz = (spaceIndex / ( nx_ * ny_ )) % nz_;
 
     vector< double > ret( 6 );
     ret[0] = x0_ + ix * dx_;
     ret[1] = y0_ + iy * dy_;
     ret[2] = z0_ + iz * dz_;
 
     ret[3] = x0_ + ix * dx_ + dx_;
     ret[4] = y0_ + iy * dy_ + dx_;
     ret[5] = z0_ + iz * dz_ + dx_;
 
     return ret;
 }

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

Definition at line 636 of file CubeMesh.cpp.

References dx_, dy_, dz_, x0_, x1_, y0_, y1_, z0_, and z1_.

Referenced by initCinfo(), and testCubeMesh().

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

Here is the caller graph for this function:

vector< double > CubeMesh::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 846 of file CubeMesh.cpp.

References dx_, dy_, dz_, EMPTY, m2s_, and neighbor().

 {
     assert( fid < m2s_.size() );
 
     vector< double > ret;
     unsigned int spaceIndex = m2s_[fid];
 
     unsigned int nIndex = neighbor( spaceIndex, 0, 0, 1 );
     if ( nIndex != EMPTY )
         ret.push_back( dx_ * dy_ );
 
     nIndex = neighbor( spaceIndex, 0, 0, -1 );
     if ( nIndex != EMPTY )
         ret.push_back( dx_ * dy_ );
 
     nIndex = neighbor( spaceIndex, 0, 1, 0 );
     if ( nIndex != EMPTY )
         ret.push_back( dz_ * dx_ );
 
     nIndex = neighbor( spaceIndex, 0, -1, 0 );
     if ( nIndex != EMPTY )
         ret.push_back( dz_ * dx_ );
 
     nIndex = neighbor( spaceIndex, 1, 0, 0 );
     if ( nIndex != EMPTY )
         ret.push_back( dy_ * dz_ );
 
     nIndex = neighbor( spaceIndex, -1, 0, 0 );
     if ( nIndex != EMPTY )
         ret.push_back( dy_ * dz_ );
 
     return ret;
 }

Here is the call graph for this function:

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

virtual

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

Implements ChemCompt.

Definition at line 881 of file CubeMesh.cpp.

 {
     return vector< double >( 6, 1.0 );
 }

double CubeMesh::getDx ( ) const

Definition at line 507 of file CubeMesh.cpp.

References dx_.

Referenced by initCinfo(), CylBase::matchCubeMeshEntries(), CylMesh::matchCubeMeshEntries(), and testCubeMesh().

 {
     return dx_;
 }

Here is the caller graph for this function:

double CubeMesh::getDy ( ) const

Definition at line 519 of file CubeMesh.cpp.

References dy_.

Referenced by initCinfo(), and testCubeMesh().

 {
     return dy_;
 }

Here is the caller graph for this function:

double CubeMesh::getDz ( ) const

Definition at line 531 of file CubeMesh.cpp.

References dz_.

Referenced by initCinfo(), and testCubeMesh().

 {
     return dz_;
 }

Here is the caller graph for this function:

bool CubeMesh::getIsToroid ( ) const

Definition at line 576 of file CubeMesh.cpp.

References isToroid_.

Referenced by initCinfo().

 {
     return isToroid_;
 }

Here is the caller graph for this function:

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

virtual

Virtual function to return dimensions of specified entry.

Implements ChemCompt.

Definition at line 778 of file CubeMesh.cpp.

Referenced by testCubeMesh(), and testCubeMeshExtendStencil().

 {
     return 3;
 }

Here is the caller graph for this function:

double CubeMesh::getMeshEntryVolume ( unsigned int fid ) const

virtual

Virtual function to return volume of mesh Entry.

Implements ChemCompt.

Definition at line 784 of file CubeMesh.cpp.

References dx_, dy_, and dz_.

 {
     return dx_ * dy_ * dz_;
 }

vector< unsigned int > CubeMesh::getMeshToSpace ( ) const

Definition at line 661 of file CubeMesh.cpp.

References m2s_.

Referenced by initCinfo(), and testCubeMeshJunctionTwoDimSurface().

 {
     return m2s_;
 }

Here is the caller graph for this function:

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

virtual

Virtual function to return MeshType of specified entry.

Implements ChemCompt.

Definition at line 772 of file CubeMesh.cpp.

References CUBOID.

Referenced by testCubeMesh(), and testCubeMeshExtendStencil().

 {
     return CUBOID;
 }

Here is the caller graph for this function:

unsigned int CubeMesh::getNx ( ) const

Definition at line 542 of file CubeMesh.cpp.

References nx_.

Referenced by initCinfo(), and testCubeMesh().

 {
     return nx_;
 }

Here is the caller graph for this function:

unsigned int CubeMesh::getNy ( ) const

Definition at line 554 of file CubeMesh.cpp.

References ny_.

Referenced by initCinfo(), and testCubeMesh().

 {
     return ny_;
 }

Here is the caller graph for this function:

unsigned int CubeMesh::getNz ( ) const

Definition at line 565 of file CubeMesh.cpp.

References nz_.

Referenced by initCinfo(), and testCubeMesh().

 {
     return nz_;
 }

Here is the caller graph for this function:

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

virtual

Inherited virtual, do nothing for now.

Implements MeshCompt.

Definition at line 905 of file CubeMesh.cpp.

References innerGetNumEntries(), and numEntries.

 {
     unsigned int numEntries = innerGetNumEntries();
     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;
 }

Here is the call graph for this function:

bool CubeMesh::getPreserveNumEntries ( ) const

Definition at line 586 of file CubeMesh.cpp.

References preserveNumEntries_.

Referenced by initCinfo().

 {
     return preserveNumEntries_;
 }

Here is the caller graph for this function:

vector< unsigned int > CubeMesh::getSpaceToMesh ( ) const

Definition at line 672 of file CubeMesh.cpp.

References s2m_.

Referenced by initCinfo(), and testCubeMeshJunctionTwoDimSurface().

 {
     return s2m_;
 }

Here is the caller graph for this function:

vector< unsigned int > CubeMesh::getSurface ( ) const

Definition at line 682 of file CubeMesh.cpp.

References surface_.

Referenced by initCinfo().

 {
     return surface_;
 }

Here is the caller graph for this function:

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

virtual

Implements MeshCompt.

Definition at line 942 of file CubeMesh.cpp.

References dx_, dy_, dz_, nx_, ny_, and nz_.

 {
     static vector< double > area;
     if ( nx_ * ny_ == 1 ) 
         area.resize( nz_, dx_ * dy_ );
     else if ( nx_ * nz_ == 1 ) 
         area.resize( ny_, dx_ * dz_ );
     else if ( ny_ * nz_ == 1 ) 
         area.resize( nx_, dy_ * dz_ );
     else
         area.resize( nx_, dy_ * dz_ ); // Just put in a number.
     assert( area.size() == nx_ * ny_ * nz_ );
     return area;
 }

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

virtual

Implements MeshCompt.

Definition at line 957 of file CubeMesh.cpp.

References dx_, dy_, dz_, and innerGetNumEntries().

 {
     static vector< double > length;
     if ( dx_ > dy_ && dx_ > dz_ )
         length.assign( innerGetNumEntries(), dx_ );
     else if ( dy_ > dz_ )
         length.assign( innerGetNumEntries(), dy_ );
     else
         length.assign( innerGetNumEntries(), dz_ );
     return length;
 }

Here is the call graph for this function:

double CubeMesh::getX0 ( ) const

Definition at line 441 of file CubeMesh.cpp.

References x0_.

Referenced by initCinfo(), and testCubeMesh().

 {
     return x0_;
 }

Here is the caller graph for this function:

double CubeMesh::getX1 ( ) const

Definition at line 474 of file CubeMesh.cpp.

References x1_.

Referenced by initCinfo(), and testCubeMesh().

 {
     return x1_;
 }

Here is the caller graph for this function:

double CubeMesh::getY0 ( ) const

Definition at line 452 of file CubeMesh.cpp.

References y0_.

Referenced by initCinfo(), and testCubeMesh().

 {
     return y0_;
 }

Here is the caller graph for this function:

double CubeMesh::getY1 ( ) const

Definition at line 485 of file CubeMesh.cpp.

References y1_.

Referenced by initCinfo(), and testCubeMesh().

 {
     return y1_;
 }

Here is the caller graph for this function:

double CubeMesh::getZ0 ( ) const

Definition at line 463 of file CubeMesh.cpp.

References z0_.

Referenced by initCinfo(), and testCubeMesh().

 {
     return z0_;
 }

Here is the caller graph for this function:

double CubeMesh::getZ1 ( ) const

Definition at line 496 of file CubeMesh.cpp.

References z1_.

Referenced by initCinfo(), and testCubeMesh().

 {
     return z1_;
 }

Here is the caller graph for this function:

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

virtual

Converts the integer meshIndex to spatial coords.

Implements ChemCompt.

Definition at line 1154 of file CubeMesh.cpp.

References dx_, dy_, dz_, nx_, ny_, nz_, x0_, y0_, and z0_.

Referenced by assignVoxels(), matchCubeMeshEntries(), and nearest().

 {
     assert ( index < nx_ * ny_ * nz_ );
 
     // index = m2s_[index];
     unsigned int ix = index % nx_;
     index /= nx_;
     unsigned int iy = index % ny_;
     index /= ny_;
     unsigned int iz = index % nz_;
 
     x = x0_ + ix * dx_ + dx_ * 0.5;
     y = y0_ + iy * dy_ + dy_ * 0.5;
     z = z0_ + iz * dz_ + dz_ * 0.5;
 }

Here is the caller graph for this function:

const Cinfo * CubeMesh::initCinfo ( )

static

Definition at line 31 of file CubeMesh.cpp.

References buildMesh(), cubeMeshCinfo, getAlwaysDiffuse(), getCoords(), getDx(), getDy(), getDz(), getIsToroid(), getMeshToSpace(), getNx(), getNy(), getNz(), getPreserveNumEntries(), getSpaceToMesh(), getSurface(), getX0(), getX1(), getY0(), getY1(), getZ0(), getZ1(), ChemCompt::initCinfo(), setAlwaysDiffuse(), setCoords(), setDx(), setDy(), setDz(), setIsToroid(), setMeshToSpace(), setNx(), setNy(), setNz(), setPreserveNumEntries(), setSpaceToMesh(), setSurface(), setX0(), setX1(), setY0(), setY1(), setZ0(), setZ1(), and surface().

 {
         // Field Definitions
         static ValueFinfo< CubeMesh, double > x0(
             "x0",
             "X coord of one end",
             &CubeMesh::setX0,
             &CubeMesh::getX0
         );
         static ValueFinfo< CubeMesh, double > y0(
             "y0",
             "Y coord of one end",
             &CubeMesh::setY0,
             &CubeMesh::getY0
         );
         static ValueFinfo< CubeMesh, double > z0(
             "z0",
             "Z coord of one end",
             &CubeMesh::setZ0,
             &CubeMesh::getZ0
         );
         static ValueFinfo< CubeMesh, double > x1(
             "x1",
             "X coord of other end",
             &CubeMesh::setX1,
             &CubeMesh::getX1
         );
         static ValueFinfo< CubeMesh, double > y1(
             "y1",
             "Y coord of other end",
             &CubeMesh::setY1,
             &CubeMesh::getY1
         );
         static ValueFinfo< CubeMesh, double > z1(
             "z1",
             "Z coord of other end",
             &CubeMesh::setZ1,
             &CubeMesh::getZ1
         );
 
         static ValueFinfo< CubeMesh, double > dx(
             "dx",
             "X size for mesh",
             &CubeMesh::setDx,
             &CubeMesh::getDx
         );
         static ValueFinfo< CubeMesh, double > dy(
             "dy",
             "Y size for mesh",
             &CubeMesh::setDy,
             &CubeMesh::getDy
         );
         static ValueFinfo< CubeMesh, double > dz(
             "dz",
             "Z size for mesh",
             &CubeMesh::setDz,
             &CubeMesh::getDz
         );
 
         static ValueFinfo< CubeMesh, unsigned int > nx(
             "nx",
             "Number of subdivisions in mesh in X",
             &CubeMesh::setNx,
             &CubeMesh::getNx
         );
         static ValueFinfo< CubeMesh, unsigned int > ny(
             "ny",
             "Number of subdivisions in mesh in Y",
             &CubeMesh::setNy,
             &CubeMesh::getNy
         );
         static ValueFinfo< CubeMesh, unsigned int > nz(
             "nz",
             "Number of subdivisions in mesh in Z",
             &CubeMesh::setNz,
             &CubeMesh::getNz
         );
 
         static ValueFinfo< CubeMesh, bool > isToroid(
             "isToroid",
             "Flag. True when the mesh should be toroidal, that is,"
             "when going beyond the right face brings us around to the"
             "left-most mesh entry, and so on. If we have nx, ny, nz"
             "entries, this rule means that the coordinate (x, ny, z)"
             "will map onto (x, 0, z). Similarly,"
             "(-1, y, z) -> (nx-1, y, z)"
             "Default is false",
             &CubeMesh::setIsToroid,
             &CubeMesh::getIsToroid
         );
 
         static ValueFinfo< CubeMesh, bool > preserveNumEntries(
             "preserveNumEntries",
             "Flag. When it is true, the numbers nx, ny, nz remain"
             "unchanged when x0, x1, y0, y1, z0, z1 are altered. Thus"
             "dx, dy, dz would change instead. When it is false, then"
             "dx, dy, dz remain the same and nx, ny, nz are altered."
             "Default is true",
             &CubeMesh::setPreserveNumEntries,
             &CubeMesh::getPreserveNumEntries
         );
 
         static ValueFinfo< CubeMesh, bool > alwaysDiffuse(
             "alwaysDiffuse",
             "Flag. When it is true, the mesh matches up sequential "
             "mesh entries for diffusion and chmestry. This is regardless "
             "of spatial location, and is guaranteed to set up at least "
             "the home reaction system"
             "Default is false",
             &CubeMesh::setAlwaysDiffuse,
             &CubeMesh::getAlwaysDiffuse
         );
 
         static ElementValueFinfo< CubeMesh, vector< double > > coords(
             "coords",
             "Set all the coords of the cuboid at once. Order is:"
             "x0 y0 z0   x1 y1 z1   dx dy dz"
             "When this is done, it recalculates the numEntries since "
             "dx, dy and dz are given explicitly."
             "As a special hack, you can leave out dx, dy and dz and use "
             "a vector of size 6. In this case the operation assumes that "
             "nx, ny and nz are to be preserved and dx, dy and dz will "
             "be recalculated. ",
             &CubeMesh::setCoords,
             &CubeMesh::getCoords
         );
 
         static ValueFinfo< CubeMesh, vector< unsigned int > > meshToSpace(
             "meshToSpace",
             "Array in which each mesh entry stores spatial (cubic) index",
             &CubeMesh::setMeshToSpace,
             &CubeMesh::getMeshToSpace
         );
 
         static ValueFinfo< CubeMesh, vector< unsigned int > > spaceToMesh(
             "spaceToMesh",
             "Array in which each space index (obtained by linearizing "
             "the xyz coords) specifies which meshIndex is present."
             "In many cases the index will store the EMPTY flag if there is"
             "no mesh entry at that spatial location",
             &CubeMesh::setSpaceToMesh,
             &CubeMesh::getSpaceToMesh
         );
 
         static ValueFinfo< CubeMesh, vector< unsigned int > > surface(
             "surface",
             "Array specifying surface of arbitrary volume within the "
             "CubeMesh. All entries must fall within the cuboid. "
             "Each entry of the array is a spatial index obtained by "
             "linearizing the ix, iy, iz coordinates within the cuboid. "
             "So, each entry == ( iz * ny + iy ) * nx + ix"
             "Note that the voxels listed on the surface are WITHIN the "
             "volume of the CubeMesh object",
             &CubeMesh::setSurface,
             &CubeMesh::getSurface
         );
 
         // MsgDest Definitions
 
         static DestFinfo buildMesh( "buildMesh",
             "Build cubical mesh for geom surface specified by Id, using"
             "specified x y z coords as an inside point in mesh",
             new OpFunc4< CubeMesh, Id, double, double, double >(
                 &CubeMesh::buildMesh )
         );
 
         // Field Elements
 
     static Finfo* cubeMeshFinfos[] = {
         &isToroid,      // Value
         &preserveNumEntries,        // Value
         &alwaysDiffuse,     // Value
         &x0,            // Value
         &y0,            // Value
         &z0,            // Value
         &x1,            // Value
         &y1,            // Value
         &z1,            // Value
         &dx,            // Value
         &dy,            // Value
         &dz,            // Value
         &nx,            // Value
         &ny,            // Value
         &nz,            // Value
         &coords,        // Value
         &meshToSpace,   // Value
         &spaceToMesh,   // Value
         &surface,       // Value
     };
 
     static string doc[] =
     {
         "Name", "CubeMesh",
         "Author", "Upi Bhalla",
         "Description", "Chemical compartment with cuboid grid. "
                 "Defaults to a cube of size 10 microns, with mesh size "
                 "also 10 microns, so that there is just 1 cubic voxel. "
                 "These defaults are similar to that of a typical cell. "
                 "Can be configured to have different x,y,z dimensions and "
                 "also different dx,dy,dz voxel sizes. ",
     };
     static Dinfo< CubeMesh > dinfo;
     static Cinfo cubeMeshCinfo (
         "CubeMesh",
         ChemCompt::initCinfo(),
         cubeMeshFinfos,
         sizeof( cubeMeshFinfos ) / sizeof ( Finfo* ),
         &dinfo,
         doc,
         sizeof(doc)/sizeof(string)
     );
 
     return &cubeMeshCinfo;
 }

Here is the call graph for this function:

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

virtual

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

Builds something as close to a cube as can get. This needs a smarter boundary handling code than I have here. For now, goes for the nearest cube

Implements ChemCompt.

Definition at line 707 of file CubeMesh.cpp.

References numEntries, nx_, ny_, nz_, and setCoords().

 {
     double approxN = numEntries;
     approxN = pow( approxN, 1.0 / 3.0 );
     unsigned int smaller = floor( approxN );
     unsigned int bigger = ceil( approxN );
     unsigned int numSide;
     if ( smaller != bigger ) {
         numSide = smaller;
     } else {
         unsigned int smallerVol = smaller * smaller * smaller;
         unsigned int biggerVol = bigger * bigger * bigger;
         if ( numEntries - smallerVol < biggerVol - numEntries )
             numSide = smaller;
         else
             numSide = bigger;
     }
     double side = pow( volume, 1.0 / 3.0 );
     vector< double > coords( 9, side );
     coords[0] = coords[1] = coords[2] = 0;
     coords[6] = coords[7] = coords[8] = side / numSide;
     nx_ = ny_ = nz_ = numSide;
     setCoords( e, coords );
 }

Here is the call graph for this function:

unsigned int CubeMesh::innerGetDimensions ( ) const

virtual

Implements ChemCompt.

Definition at line 687 of file CubeMesh.cpp.

 {
     return 3;
 }

unsigned int CubeMesh::innerGetNumEntries ( ) const

virtual

Inherited virtual func. Returns number of MeshEntry in array

Implements ChemCompt.

Definition at line 891 of file CubeMesh.cpp.

References m2s_.

Referenced by getParentVoxel(), getVoxelLength(), and testCubeMesh().

 {
     return m2s_.size();
 }

Here is the caller graph for this function:

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

virtual

Generate node decomposition of mesh, send it out along meshSplitFinfo msg

Implements ChemCompt.

Definition at line 743 of file CubeMesh.cpp.

 {
     /*
     unsigned int numEntries = nx_ * ny_ * nz_ ;
     vector< double > vols( numEntries, dx_ * dy_ * dz_ );
     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 CubeMesh::innerHandleRequestMeshStats	(	const Eref &	e,
		const SrcFinfo2< unsigned int, vector< double > > *	meshStatsFinfo
	)

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

Definition at line 734 of file CubeMesh.cpp.

References dx_, dy_, dz_, nx_, ny_, and nz_.

 {
     vector< double > meshVolumes( 1, dx_ * dy_ * dz_ );
     meshStatsFinfo->send( e, nx_ * ny_ * nz_, meshVolumes);
 }

void CubeMesh::innerSetCoords ( const vector< double > & v )

Definition at line 602 of file CubeMesh.cpp.

References dx_, dy_, dz_, preserveNumEntries_, updateCoords(), x0_, x1_, y0_, y1_, z0_, and z1_.

Referenced by setCoords(), testCubeMesh(), testCubeMeshExtendStencil(), testCubeMeshFillTwoDimSurface(), testCubeMeshJunctionDiffSizeMesh(), testCubeMeshJunctionTwoDimSurface(), and testCubeMeshMultiJunctionTwoD().

 {
     if ( v.size() < 6 )
         return;
 
     x0_ = v[0];
     y0_ = v[1];
     z0_ = v[2];
 
     x1_ = v[3];
     y1_ = v[4];
     z1_ = v[5];
 
     bool temp = preserveNumEntries_;
     if ( v.size() >= 9 ) {
         dx_ = v[6];
         dy_ = v[7];
         dz_ = v[8];
         preserveNumEntries_ = 0;
     } else {
         preserveNumEntries_ = 1;
     }
     updateCoords();
     preserveNumEntries_ = temp;
 
 }

Here is the call graph for this function:

Here is the caller graph for this function:

void CubeMesh::innerSetNumEntries ( unsigned int n )

virtual

Inherited virtual func.

Inherited virtual func. Assigns number of MeshEntries.

Implements ChemCompt.

Definition at line 899 of file CubeMesh.cpp.

 {
     cout << "Warning: CubeMesh::innerSetNumEntries is readonly.\n";
 }

bool CubeMesh::isInsideCuboid	(	double	x,
		double	y,
		double	z
	)		const

Definition at line 986 of file CubeMesh.cpp.

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

Referenced by fillSpaceToMeshLookup().

 {
         return ( x >= x0_ && x < x1_ && y >= y0_ && y < y1_ &&
                         z >= z0_ && z < z1_ );
 }

Here is the caller graph for this function:

bool CubeMesh::isInsideSpheroid	(	double	x,
		double	y,
		double	z
	)		const

Definition at line 992 of file CubeMesh.cpp.

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

 {
     double cx = ( x0_ + x1_ ) / 2.0;
     double cy = ( y0_ + y1_ ) / 2.0;
     double cz = ( z0_ + z1_ ) / 2.0;
 
     double rx = ( x - cx ) / fabs( x1_ - x0_ ) / 2.0;
     double ry = ( y - cy ) / fabs( y1_ - y0_ ) / 2.0;
     double rz = ( z - cz ) / fabs( z1_ - z0_ ) / 2.0;
 
     return ( ( rx * rx + ry * ry + rz * rz ) < 1.0 );
 }

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

Dumbed-down version that does mesh matching based only on index. Useful for non-spatial matching and single-voxel systems.

Version that assumes all voxels are in contact and able to diffuse with matching voxels on other mesh

Definition at line 1503 of file CubeMesh.cpp.

References m2s_.

Referenced by matchMeshEntries().

 {
     ret.clear();
     unsigned int min = m2s_.size();
     if ( min > other->m2s_.size() )
         min = other->m2s_.size();
     ret.resize( min );
     for ( unsigned int i = 0; i < min; ++i ) {
         ret[i] = VoxelJunction( i, i );
     }
 }

Here is the caller graph for this function:

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

Specialization for cube-to-cube mesh matching. Return vector is of pairs of meshIndices (not spatialIndices).

Definition at line 1453 of file CubeMesh.cpp.

References assignVoxels(), checkAbut(), compareMeshSpacing(), defineIntersection(), dx_, dy_, dz_, EMPTY, ChemCompt::flipRet(), indexToSpace(), matchMeshEntries(), s2m_, setDiffScale(), setJunctionVol(), and surface_.

Referenced by matchMeshEntries(), testCubeMeshJunctionDiffSizeMesh(), and testCubeMeshJunctionTwoDimSurface().

 {
         // Flip meshes if the current grid is finer.
         // There are still problems here because a finer grid will end
         // up with 2 levels deep defined as being abutting.
     if ( compareMeshSpacing( other ) == -1 ) {
             other->matchMeshEntries( this, ret );
             flipRet( ret );
             return;
     }
     ret.resize( 0 );
     // Define intersecting cuboid
     double xmin, xmax, ymin, ymax, zmin, zmax;
     defineIntersection( other, xmin, xmax, ymin, ymax, zmin, zmax );
 
     // Allocate intersecting cuboid
     unsigned int nx = 0.5 + ( xmax - xmin ) / dx_;
     unsigned int ny = 0.5 + ( ymax - ymin ) / dy_;
     unsigned int nz = 0.5 + ( zmax - zmin ) / dz_;
     vector< PII > intersect( nx * ny * nz, PII( EMPTY, EMPTY ) );
     assignVoxels( intersect, xmin, xmax, ymin, ymax, zmin, zmax );
 
     // Scan through finer mesh surface, check for occupied voxels.
     for ( vector< unsigned int >::const_iterator i =
                     other->surface_.begin();
                     i != other->surface_.end(); ++i ) {
         double x, y, z;
         other->indexToSpace( *i, x, y, z );
         if ( x >= xmin && x <= xmax && y >= ymin && y <= ymax &&
                         z >= zmin && z <= zmax ) {
             unsigned int ix = ( x - xmin ) / dx_;
             unsigned int iy = ( y - ymin ) / dy_;
             unsigned int iz = ( z - zmin ) / dz_;
             unsigned int meshIndex = other->s2m_[ *i ];
             checkAbut( intersect, ix, iy, iz, nx, ny, nz, meshIndex, ret );
         }
     }
 
     // Scan through the VoxelJunctions and populate their diffScale field
     setDiffScale( other, ret );
     // Scan through the VoxelJunctions and populate their volume field
     setJunctionVol( other, ret );
     sort( ret.begin(), ret.end() );
 }

Here is the call graph for this function:

Here is the caller graph for this function:

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

Definition at line 1516 of file CubeMesh.cpp.

References ChemCompt::flipRet(), and ChemCompt::matchMeshEntries().

 {
     other->matchMeshEntries( this, ret );
     flipRet( ret );
 }

Here is the call graph for this function:

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

virtual

Key virtual function for generating a map between facing surfaces on a CubeMesh and another ChemCompt

Implements ChemCompt.

Definition at line 1118 of file CubeMesh.cpp.

References alwaysDiffuse_, ChemCompt::flipRet(), matchAllEntries(), matchCubeMeshEntries(), and EndoMesh::matchMeshEntries().

Referenced by matchCubeMeshEntries().

 {
     const CubeMesh* cm = dynamic_cast< const CubeMesh* >( other );
 
     if ( cm ) {
         if ( alwaysDiffuse_ )
             matchAllEntries( cm, ret );
         else
             matchCubeMeshEntries( cm, ret );
         /*
         if ( compareMeshSpacing( cm ) == 0 ) { // Equal spacing.
                 matchSameSpacing( cm, ret );
         } else if ( compareMeshSpacing( cm ) == -1 ) { // self is finer
                 cout << "Warning:CubeMesh::matchMeshEntries: cannot yet handle unequal meshes\n";
         } else { // other is finer.
                 cout << "Warning:CubeMesh::matchMeshEntries: cannot yet handle unequal meshes\n";
         }
         */
         return;
     }
     const EndoMesh* em = dynamic_cast< const EndoMesh* >( other );
     if ( em ) {
         em->matchMeshEntries( this, ret );
         flipRet( ret );
         return;
     }
     cout << "Warning:CubeMesh::matchMeshEntries: cannot yet handle Neuro or Cyl meshes.\n";
 }

Here is the call graph for this function:

Here is the caller graph for this function:

double CubeMesh::nearest	(	double	x,
		double	y,
		double	z,
		unsigned int &	index
	)		const

virtual

Virtual function to return the distance and index of nearest meshEntry. Places entry at centre of voxel.

Implements ChemCompt.

Definition at line 1185 of file CubeMesh.cpp.

References ChemCompt::distance(), dx_, dy_, dz_, EMPTY, indexToSpace(), nx_, ny_, s2m_, surface_, x0_, y0_, z0_, and z1_.

 {
     if ( x > x0_ && x < x1_ && y > y0_ && y < y1_ && z > z0_ && z < z1_ )
     {
         unsigned int ix = ( x - x0_ ) / dx_;
         unsigned int iy = ( y - y0_ ) / dy_;
         unsigned int iz = ( z - z0_ ) / dz_;
         index = ( iz * ny_ + iy ) * nx_ + ix;
         unsigned int innerIndex = s2m_[ index ];
         if ( innerIndex != EMPTY ) { // Inside filled volume
             index = innerIndex;
             double tx = x0_ + ix * dx_ + dx_ * 0.5;
             double ty = y0_ + iy * dy_ + dy_ * 0.5;
             double tz = z0_ + iz * dz_ + dz_ * 0.5;
             return distance( x - tx, y - ty, z - tz );
         } else { // Outside volume. Look over surface for nearest.
             double rmin = 1e99;
             for ( vector< unsigned int >::const_iterator
                 i = surface_.begin(); i != surface_.end(); ++i )
             {
                 double tx, ty, tz;
                 indexToSpace( *i, tx, ty, tz );
                 double r = distance( tx - x, ty - y, tz - z );
                 if ( rmin > r ) {
                         rmin = r;
                         index = *i;
                 }
             }
             return -rmin; // Negative distance indicates xyz is outside vol
         }
     }
     // Should really figure out nearest corner anyway.
     index = 0;
     return -1.0;
 }

Here is the call graph for this function:

unsigned int CubeMesh::neighbor	(	unsigned int	spaceIndex,
		int	dx,
		int	dy,
		int	dz
	)		const

Definition at line 822 of file CubeMesh.cpp.

References EMPTY, nx_, ny_, nz_, and s2m_.

Referenced by getDiffusionArea().

 {
     int ix = spaceIndex % nx_;
     int iy = (spaceIndex / nx_) % ny_;
     int iz = (spaceIndex / ( nx_ * ny_ )) % nz_;
 
     ix += dx;
     iy += dy;
     iz += dz;
 
     if ( ix < 0 || ix >= static_cast< int >( nx_ ) )
         return EMPTY;
     if ( iy < 0 || iy >= static_cast< int >( ny_ ) )
         return EMPTY;
     if ( iz < 0 || iz >= static_cast< int >( nz_ ) )
         return EMPTY;
 
     unsigned int nIndex = ( ( iz * ny_ ) + iy ) * nx_ + ix;
 
     return s2m_[nIndex];
 }

Here is the caller graph for this function:

unsigned int CubeMesh::numDims ( ) const

Utility function for returning # of dimensions in mesh.

Definition at line 1148 of file CubeMesh.cpp.

References nx_, ny_, and nz_.

Referenced by testCubeMeshFillTwoDimSurface().

 {
     return ( ( nx_ > 1 ) + ( ny_ > 1 ) + ( nz_ > 1 ) );
 }

Here is the caller graph for this function:

void CubeMesh::setAlwaysDiffuse ( bool v )

Definition at line 591 of file CubeMesh.cpp.

References alwaysDiffuse_.

Referenced by initCinfo().

 {
     alwaysDiffuse_ = v;
 }

Here is the caller graph for this function:

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

Definition at line 629 of file CubeMesh.cpp.

References innerSetCoords(), vGetVoxelVolume(), and ChemCompt::voxelVolOut().

Referenced by initCinfo(), and innerBuildDefaultMesh().

 {
     // double oldVol = getMeshEntryVolume( 0 );
     innerSetCoords( v );
     ChemCompt::voxelVolOut()->send( e, vGetVoxelVolume() );
 }

Here is the call graph for this function:

Here is the caller graph for this function:

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

Assigns diffusion scaling info for the voxel junctions.

Definition at line 1523 of file CubeMesh.cpp.

References doubleEq(), dx_, dy_, and dz_.

Referenced by matchCubeMeshEntries().

 {
 
     for ( vector< VoxelJunction >::iterator i = ret.begin();
                     i != ret.end(); ++i )
     {
         if ( doubleEq( i->diffScale, 0 ) ) { // Junction across x plane
             double selfXA = dy_ * dz_;
             double otherXA = other->dy_ * other->dz_;
             if ( selfXA <= otherXA )
                 i->diffScale = 2 * selfXA / ( dx_ + other->dx_ );
             else
                 i->diffScale = 2 * otherXA / ( dx_ + other->dx_ );
         } else if ( doubleEq( i->diffScale, 1 ) ) { // across y plane
             double selfXA = dx_ * dz_;
             double otherXA = other->dx_ * other->dz_;
             if ( selfXA <= otherXA )
                 i->diffScale = 2 * selfXA / ( dy_ + other->dy_ );
             else
                 i->diffScale = 2 * otherXA / ( dy_ + other->dy_ );
         } else if ( doubleEq( i->diffScale, 2 ) ) { // across z plane
             double selfXA = dx_ * dy_;
             double otherXA = other->dx_ * other->dy_;
             if ( selfXA <= otherXA )
                 i->diffScale = 2 * selfXA / ( dz_ + other->dz_ );
             else
                 i->diffScale = 2 * otherXA / ( dz_ + other->dz_ );
         } else {
             assert( 0 );
         }
     }
 }

Here is the call graph for this function:

Here is the caller graph for this function:

void CubeMesh::setDx ( double v )

Definition at line 501 of file CubeMesh.cpp.

References dx_, and updateCoords().

Referenced by initCinfo().

 {
     dx_ = v;
     updateCoords();
 }

Here is the call graph for this function:

Here is the caller graph for this function:

void CubeMesh::setDy ( double v )

Definition at line 513 of file CubeMesh.cpp.

References dy_, and updateCoords().

Referenced by initCinfo().

 {
     dy_ = v;
     updateCoords();
 }

Here is the call graph for this function:

Here is the caller graph for this function:

void CubeMesh::setDz ( double v )

Definition at line 525 of file CubeMesh.cpp.

References dz_, and updateCoords().

Referenced by initCinfo().

 {
     dz_ = v;
     updateCoords();
 }

Here is the call graph for this function:

Here is the caller graph for this function:

void CubeMesh::setIsToroid ( bool v )

Definition at line 571 of file CubeMesh.cpp.

References isToroid_.

Referenced by initCinfo().

 {
     isToroid_ = v;
 }

Here is the caller graph for this function:

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

Assigns volume info for the voxel junctions.

Definition at line 1557 of file CubeMesh.cpp.

References dx_, dy_, and dz_.

Referenced by matchCubeMeshEntries().

 {
 
     double myVol = dx_ * dy_ * dz_;
     double otherVol = other->dx_ * other->dy_ * other->dz_;
     for ( vector< VoxelJunction >::iterator i = ret.begin();
                     i != ret.end(); ++i )
     {
         i->firstVol = myVol;
         i->secondVol = otherVol;
     }
 }

Here is the caller graph for this function:

void CubeMesh::setMeshToSpace ( vector< unsigned int > v )

Definition at line 655 of file CubeMesh.cpp.

References deriveS2mFromM2s(), and m2s_.

Referenced by initCinfo(), and testCubeMeshJunctionTwoDimSurface().

 {
     m2s_ = v;
     deriveS2mFromM2s();
 }

Here is the call graph for this function:

Here is the caller graph for this function:

void CubeMesh::setNx ( unsigned int v )

Definition at line 536 of file CubeMesh.cpp.

References nx_, and updateCoords().

Referenced by initCinfo().

 {
     nx_ = v;
     updateCoords();
 }

Here is the call graph for this function:

Here is the caller graph for this function:

void CubeMesh::setNy ( unsigned int v )

Definition at line 548 of file CubeMesh.cpp.

References ny_, and updateCoords().

Referenced by initCinfo().

 {
     ny_ = v;
     updateCoords();
 }

Here is the call graph for this function:

Here is the caller graph for this function:

void CubeMesh::setNz ( unsigned int v )

Definition at line 559 of file CubeMesh.cpp.

References nz_, and updateCoords().

Referenced by initCinfo().

 {
     nz_ = v;
     updateCoords();
 }

Here is the call graph for this function:

Here is the caller graph for this function:

void CubeMesh::setPreserveNumEntries ( bool v )

Definition at line 581 of file CubeMesh.cpp.

References preserveNumEntries_.

Referenced by initCinfo(), testCubeMesh(), testCubeMeshExtendStencil(), testCubeMeshFillTwoDimSurface(), testCubeMeshJunctionDiffSizeMesh(), testCubeMeshJunctionTwoDimSurface(), and testCubeMeshMultiJunctionTwoD().

 {
     preserveNumEntries_ = v;
 }

Here is the caller graph for this function:

void CubeMesh::setSpaceToMesh ( vector< unsigned int > v )

Definition at line 666 of file CubeMesh.cpp.

References deriveM2sFromS2m(), and s2m_.

Referenced by initCinfo(), and testCubeMeshJunctionTwoDimSurface().

 {
     s2m_ = v;
     deriveM2sFromS2m();
 }

Here is the call graph for this function:

Here is the caller graph for this function:

void CubeMesh::setSurface ( vector< unsigned int > v )

Definition at line 677 of file CubeMesh.cpp.

References surface_.

Referenced by initCinfo(), and testCubeMeshJunctionTwoDimSurface().

 {
     surface_ = v;
 }

Here is the caller graph for this function:

void CubeMesh::setX0 ( double v )

Definition at line 435 of file CubeMesh.cpp.

References updateCoords(), and x0_.

Referenced by initCinfo(), and testCubeMesh().

 {
     x0_ = v;
     updateCoords();
 }

Here is the call graph for this function:

Here is the caller graph for this function:

void CubeMesh::setX1 ( double v )

Definition at line 468 of file CubeMesh.cpp.

References updateCoords(), and x1_.

Referenced by initCinfo(), and testCubeMesh().

 {
     x1_ = v;
     updateCoords();
 }

Here is the call graph for this function:

Here is the caller graph for this function:

void CubeMesh::setY0 ( double v )

Definition at line 446 of file CubeMesh.cpp.

References updateCoords(), and y0_.

Referenced by initCinfo(), and testCubeMesh().

 {
     y0_ = v;
     updateCoords();
 }

Here is the call graph for this function:

Here is the caller graph for this function:

void CubeMesh::setY1 ( double v )

Definition at line 479 of file CubeMesh.cpp.

References updateCoords(), and y1_.

Referenced by initCinfo(), and testCubeMesh().

 {
     y1_ = v;
     updateCoords();
 }

Here is the call graph for this function:

Here is the caller graph for this function:

void CubeMesh::setZ0 ( double v )

Definition at line 457 of file CubeMesh.cpp.

References updateCoords(), and z0_.

Referenced by initCinfo(), and testCubeMesh().

 {
     z0_ = v;
     updateCoords();
 }

Here is the call graph for this function:

Here is the caller graph for this function:

void CubeMesh::setZ1 ( double v )

Definition at line 490 of file CubeMesh.cpp.

References updateCoords(), and z1_.

Referenced by initCinfo(), and testCubeMesh().

 {
     z1_ = v;
     updateCoords();
 }

Here is the call graph for this function:

Here is the caller graph for this function:

unsigned int CubeMesh::spaceToIndex	(	double	x,
		double	y,
		double	z
	)		const

Converts the 3-D coords to an index. EMPTY if out of range.

Definition at line 1171 of file CubeMesh.cpp.

References dx_, dy_, dz_, EMPTY, nx_, ny_, s2m_, x0_, y0_, z0_, and z1_.

Referenced by fillPointsOnCircle(), and fillPointsOnDisc().

 {
     if ( x > x0_ && x < x1_ && y > y0_ && y < y1_ && z > z0_ && z < z1_ )
     {
         unsigned int ix = ( x - x0_ ) / dx_;
         unsigned int iy = ( y - y0_ ) / dy_;
         unsigned int iz = ( z - z0_ ) / dz_;
         unsigned int index = ( iz * ny_ + iy ) * nx_ + ix;
         unsigned int innerIndex = s2m_[ index ];
         return innerIndex;
     }
     return EMPTY;
 }

Here is the caller graph for this function:

const vector< unsigned int > & CubeMesh::surface ( ) const

Utility and test function to read surface.

Definition at line 1111 of file CubeMesh.cpp.

References surface_.

Referenced by initCinfo(), testCubeMeshFillTwoDimSurface(), testCubeMeshJunctionDiffSizeMesh(), testCubeMeshJunctionTwoDimSurface(), and testCubeMeshMultiJunctionTwoD().

 {
     return surface_;
 }

Here is the caller graph for this function:

void CubeMesh::transmitChange	(	const Eref &	e,
		double	oldvol
	)

void CubeMesh::updateCoords ( )

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

This assumes that dx, dy, dz are the quantities to preserve, over numEntries. So when the compartment changes volume, so does numEntries. dx, dy, dz do not change, some of the sub-cuboids will partially be outside.

Temporarily fill out the whole cube for m2s and s2m. These

Definition at line 384 of file CubeMesh.cpp.

References buildStencil(), dx_, dy_, dz_, fillThreeDimSurface(), m2s_, nx_, ny_, nz_, preserveNumEntries_, s2m_, surface_, swapIfBackward(), x0_, x1_, y0_, y1_, z0_, and z1_.

Referenced by CubeMesh(), innerSetCoords(), setDx(), setDy(), setDz(), setNx(), setNy(), setNz(), setX0(), setX1(), setY0(), setY1(), setZ0(), and setZ1().

 {
     swapIfBackward( x0_, x1_ );
     swapIfBackward( y0_, y1_ );
     swapIfBackward( z0_, z1_ );
     if ( preserveNumEntries_ ) {
         dx_ = ( x1_ - x0_ ) / nx_;
         dy_ = ( y1_ - y0_ ) / ny_;
         dz_ = ( z1_ - z0_ ) / nz_;
     } else {
         nx_ = round( (x1_ - x0_) / dx_ );
         ny_ = round( (y1_ - y0_) / dy_ );
         nz_ = round( (z1_ - z0_) / dz_ );
 
         if ( nx_ == 0 ) nx_ = 1;
         if ( ny_ == 0 ) ny_ = 1;
         if ( nz_ == 0 ) nz_ = 1;
     }
 
     // will change for none-cube geometries.
     unsigned int size = nx_ * ny_ * nz_;
     m2s_.resize( size );
     s2m_.resize( size );
     for ( unsigned int i = 0; i < size; ++i ) {
         m2s_[i] = s2m_[i] = i;
     }
 
     // Fill out surface vector
     surface_.resize( 0 );
     /*
     if ( numDims() == 0 ) {
         surface_.push_back( 0 );
     } else if ( numDims() == 1 ) {
         surface_.push_back( 0 );
         if ( size > 1 )
             surface_.push_back( size - 1 );
     } else if ( numDims() == 2 ) {
         fillTwoDimSurface();
     } else if ( numDims() == 3 ) {
         fillThreeDimSurface();
     }
     */
     fillThreeDimSurface();
 
     // volume_ = ( x1_ - x0_ ) * ( y1_ - y0_ ) * ( z1_ - z0_ );
     assert( size >= 0 );
 
     buildStencil();
 }

Here is the call graph for this function:

Here is the caller graph for this function:

void CubeMesh::updateM2s ( )

void CubeMesh::updateS2m ( )

double CubeMesh::vGetEntireVolume ( ) const

virtual

Virtual func to get volume of entire compartment.

Implements ChemCompt.

Definition at line 761 of file CubeMesh.cpp.

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

Referenced by vSetVolumeNotRates().

 {
     return fabs( (x1_ - x0_) * (y1_ - y0_) * (z1_ - z0_) );
 }

Here is the caller graph for this function:

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

virtual

Virtual func so that derived classes can return voxel midpoint.

Implements ChemCompt.

Definition at line 925 of file CubeMesh.cpp.

References dx_, dy_, dz_, m2s_, nx_, ny_, x0_, y0_, and z0_.

 {
     static vector< double > midpoint;
     midpoint.resize( m2s_.size() * 3 );
     for ( unsigned int i = 0; i < m2s_.size(); ++i ) // x coords. Lowest.
         midpoint[i] = x0_ + ( 0.5 + (m2s_[i] % nx_ ) ) * dx_;
     for ( unsigned int i = 0; i < m2s_.size(); ++i ) { // y coords. Middle.
         unsigned int k = i + m2s_.size();
         midpoint[k] = y0_ + ( 0.5 + ( (m2s_[i] / nx_) % ny_ ) ) * dy_;
     }
     for ( unsigned int i = 0; i < m2s_.size(); ++i ) { // z coords. Top.
         unsigned int k = i + m2s_.size() * 2;
         midpoint[k] = z0_ + ( 0.5 + ( m2s_[i] / ( nx_ * ny_ ) ) ) * dz_;
     }
     return midpoint;
 }

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

virtual

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

Implements ChemCompt.

Definition at line 917 of file CubeMesh.cpp.

References dx_, dy_, dz_, nx_, ny_, and nz_.

Referenced by setCoords().

 {
     static vector< double > vol;
     vol.clear();
     vol.resize( nx_ * ny_ * nz_, dx_ * dy_ * dz_ );
     return vol;
 }

Here is the caller graph for this function:

bool CubeMesh::vSetVolumeNotRates ( double volume )

virtual

Virtual func, assigns volume, usually to single voxel.

Implements ChemCompt.

Definition at line 969 of file CubeMesh.cpp.

References dx_, dy_, dz_, vGetEntireVolume(), x0_, x1_, y0_, y1_, z0_, and z1_.

 {
     // Leave x0,y0.z0 and nx,ny,nz the same. Do NOT update any rates.
     double oldvol = vGetEntireVolume();
     double linscale = pow( vol / oldvol , 1.0 / 3.0 );
     dx_ *= linscale;
     dy_ *= linscale;
     dz_ *= linscale;
     x1_ = x0_ + dx_;
     y1_ = y0_ + dy_;
     z1_ = z0_ + dz_;
 
     return true;
 }

Here is the call graph for this function:

Member Data Documentation

const unsigned int CubeMesh::ABUTX = ~2

static

Definition at line 287 of file CubeMesh.h.

Referenced by checkAbut(), setIntersectVoxel(), and testIntersectVoxel().

const unsigned int CubeMesh::ABUTY = ~3

static

Definition at line 288 of file CubeMesh.h.

Referenced by checkAbut(), and setIntersectVoxel().

const unsigned int CubeMesh::ABUTZ = ~4

static

Definition at line 289 of file CubeMesh.h.

Referenced by checkAbut(), and setIntersectVoxel().

bool CubeMesh::alwaysDiffuse_

private

Flag: Should dx change or nx, with vol?

Definition at line 297 of file CubeMesh.h.

Referenced by getAlwaysDiffuse(), matchMeshEntries(), and setAlwaysDiffuse().

double CubeMesh::dx_

private

double CubeMesh::dy_

private

Cuboid edge.

Definition at line 308 of file CubeMesh.h.

Referenced by assignVoxels(), buildStencil(), compareMeshSpacing(), defineIntersection(), extendedMeshEntryVolume(), fillSpaceToMeshLookup(), getCoordinates(), getCoords(), getDiffusionArea(), getDy(), getMeshEntryVolume(), getVoxelArea(), getVoxelLength(), indexToSpace(), innerHandleRequestMeshStats(), innerSetCoords(), matchCubeMeshEntries(), nearest(), setDiffScale(), setDy(), setJunctionVol(), spaceToIndex(), updateCoords(), vGetVoxelMidpoint(), vGetVoxelVolume(), and vSetVolumeNotRates().

double CubeMesh::dz_

private

Cuboid edge.

Definition at line 309 of file CubeMesh.h.

Referenced by assignVoxels(), buildStencil(), compareMeshSpacing(), defineIntersection(), extendedMeshEntryVolume(), fillSpaceToMeshLookup(), getCoordinates(), getCoords(), getDiffusionArea(), getDz(), getMeshEntryVolume(), getVoxelArea(), getVoxelLength(), indexToSpace(), innerHandleRequestMeshStats(), innerSetCoords(), matchCubeMeshEntries(), nearest(), setDiffScale(), setDz(), setJunctionVol(), spaceToIndex(), updateCoords(), vGetVoxelMidpoint(), vGetVoxelVolume(), and vSetVolumeNotRates().

const unsigned int CubeMesh::EMPTY = ~0

static

Definition at line 285 of file CubeMesh.h.

Referenced by buildStencil(), checkAbut(), deriveM2sFromS2m(), deriveS2mFromM2s(), fillPointsOnCircle(), fillPointsOnDisc(), fillSpaceToMeshLookup(), getDiffusionArea(), matchCubeMeshEntries(), nearest(), neighbor(), setAbut(), spaceToIndex(), and testIntersectVoxel().

bool CubeMesh::isToroid_

private

Definition at line 295 of file CubeMesh.h.

Referenced by getIsToroid(), and setIsToroid().

vector< unsigned int > CubeMesh::m2s_

private

of entries in z in surround volume

For spherical mesh, coords are xyz r0 r1 theta0 theta1 phi0 phi1 For Cylindrical mesh, coords are x1y1z1 x2y2z2 r0 r1 phi0 phi1 For cuboid mesh, coords are x1y1z1 x2y2z2 For tetrahedral mesh, coords are x1y1z1 x2y2z2 x3y3z3 x4y4z4 Later worry about planar meshes. Those would be surfaces Mesh to Space lookup. Indexed by linear mesh index, from 0 to number of actual mesh entries (occupied cuboids). Returns spatial index, from 0 to nx * ny * nz - 1. Needed whenever the cuboid mesh is not filling the entire volume of the cube, that is, in most cases.

Definition at line 330 of file CubeMesh.h.

Referenced by buildStencil(), deriveM2sFromS2m(), deriveS2mFromM2s(), extendedMeshEntryVolume(), fillSpaceToMeshLookup(), getCoordinates(), getDiffusionArea(), getMeshToSpace(), innerGetNumEntries(), matchAllEntries(), setMeshToSpace(), updateCoords(), and vGetVoxelMidpoint().

const unsigned int CubeMesh::MULTI = ~5

static

Definition at line 290 of file CubeMesh.h.

Referenced by checkAbut(), setAbut(), and testIntersectVoxel().

unsigned int CubeMesh::nx_

private

Cuboid edge.

Definition at line 311 of file CubeMesh.h.

Referenced by assignVoxels(), buildStencil(), deriveM2sFromS2m(), deriveS2mFromM2s(), fillSpaceToMeshLookup(), fillThreeDimSurface(), fillTwoDimSurface(), getCoordinates(), getNx(), getVoxelArea(), indexToSpace(), innerBuildDefaultMesh(), innerHandleRequestMeshStats(), nearest(), neighbor(), numDims(), setNx(), spaceToIndex(), updateCoords(), vGetVoxelMidpoint(), and vGetVoxelVolume().

unsigned int CubeMesh::ny_

private

of entries in x in surround volume

Definition at line 312 of file CubeMesh.h.

Referenced by assignVoxels(), buildStencil(), deriveM2sFromS2m(), deriveS2mFromM2s(), fillSpaceToMeshLookup(), fillThreeDimSurface(), fillTwoDimSurface(), getCoordinates(), getNy(), getVoxelArea(), indexToSpace(), innerBuildDefaultMesh(), innerHandleRequestMeshStats(), nearest(), neighbor(), numDims(), setNy(), spaceToIndex(), updateCoords(), vGetVoxelMidpoint(), and vGetVoxelVolume().

unsigned int CubeMesh::nz_

private

of entries in y in surround volume

Definition at line 313 of file CubeMesh.h.

Referenced by assignVoxels(), buildStencil(), deriveM2sFromS2m(), deriveS2mFromM2s(), fillSpaceToMeshLookup(), fillThreeDimSurface(), fillTwoDimSurface(), getCoordinates(), getNz(), getVoxelArea(), indexToSpace(), innerBuildDefaultMesh(), innerHandleRequestMeshStats(), neighbor(), numDims(), setNz(), updateCoords(), and vGetVoxelVolume().

bool CubeMesh::preserveNumEntries_

private

Flag: Should the ends loop around mathemagically?

Definition at line 296 of file CubeMesh.h.

Referenced by getPreserveNumEntries(), innerSetCoords(), setPreserveNumEntries(), and updateCoords().

vector< unsigned int > CubeMesh::s2m_

private

Space to Mesh lookup. Indexed by spatial index, from 0 to nx * ny * nz - 1. Specifically, point x y z is indexed as ( z * ny + y ) * nx + x. Returns mesh index to look up molecules etc in the specific volume. In case the spatial location is outside the included volume of the mesh, returns ~0.

Definition at line 339 of file CubeMesh.h.

Referenced by assignVoxels(), buildStencil(), deriveM2sFromS2m(), deriveS2mFromM2s(), fillSpaceToMeshLookup(), getSpaceToMesh(), matchCubeMeshEntries(), nearest(), neighbor(), setSpaceToMesh(), spaceToIndex(), and updateCoords().