MeshEntry

class MeshEntry

One voxel in a chemical reaction compartment

proc

void (shared message field) Shared message for process and reinit

mesh

void (shared message field) Shared message for updating mesh volumes and subdivisions,typically controls pool volumes

getVolume()

(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.

getDimensions()

(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.

getMeshType()

(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.

getCoordinates()

(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.

getNeighbors()

(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.

getDiffusionArea()

(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.

getDiffusionScaling()

(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.

process()

(destination message field) Handles process call

reinit()

(destination message field) Handles reinit call

getVolume()

(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.

remeshOut

double,unsigned int,unsigned int,vector<unsigned int>,vector<double> (source message field) Tells the target pool or other entity that the compartment subdivision(meshing) has changed, and that it has to redo its volume and memory allocation accordingly.Arguments are: oldvol, numTotalEntries, startEntry, localIndices, volsThe vols specifies volumes of each local mesh entry. It also specifieshow many meshEntries are present on the local node.The localIndices vector is used for general load balancing only.It has a list of the all meshEntries on current node.If it is empty, we assume block load balancing. In this secondcase the contents of the current node go from startEntry to startEntry + vols.size().

remeshReacsOut

void (source message field) Tells connected enz or reac that the compartment subdivision(meshing) has changed, and that it has to redo its volume-dependent rate terms like numKf_ accordingly.

volume

double (value field) Volume of this MeshEntry

dimensions

unsigned int (value field) number of dimensions of this MeshEntry

meshType

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

Coordinates

vector<double> (value field) Coordinates that define current MeshEntry. Depend on MeshType.

neighbors

vector<unsigned int> (value field) Indices of other MeshEntries that this one connects to

DiffusionArea

vector<double> (value field) Diffusion area for geometry of interface

DiffusionScaling

vector<double> (value field) Diffusion scaling for geometry of interface