org.catacomb.numeric.difnet

Interface DiffusionCalculator

All Known Implementing Classes:

NetDiffuser

public interface DiffusionCalculator

diffusion on full or a-cyclic networks. An example of the latter is an isolated neurons in an isopotential baths. Loosely called a cable solver. Implementations should check for and, where possible, exploit, the absence of loops, as with some form of sparse in-place matrix solution (cf Hines Method). When applied to neurons, the diffusing quantity may be the voltage or a diffusible specie.

Method Summary

Methods

Modifier and Type	Method and Description
void	advance(NetState dn, DiffusibleQuantity dq, Timestep ts) Run the diffusion calculation for the supplied network, diffusible quantity and timestep.
void	init(NetStructure dnet) Initialises the internal representation of the network structure.

Method Detail

init

void init(NetStructure dnet)

Initialises the internal representation of the network structure. In general this nethod will only be called once, possibly by the constructor. All geometry specific but value independent calculation can be done here. Subsequent callse to diffuse use the same precomputed mapping.

Parameters:

dnet - the diffusive net properties defining the network geometry.

advance

void advance(NetState dn,
           DiffusibleQuantity dq,
           Timestep ts)

Run the diffusion calculation for the supplied network, diffusible quantity and timestep. The values in the DiffusiveNet are read with getValue(DiffusibleQuantity) and set after the calculation with setValue(DiffusibleQuantity, double)

Parameters:

difnet - the NetState to evolve. Note that its structure object must be the same as that used to initialise the net diffuser.

dq - the diffusible quantity to use. One net may contain several different diffusing quantitites - membrane potential, ions, indicators and others. NB as yet dq is ignored MISSING

timestep - the timestep to be taken

Throws:

something - if the NetState's structure doesnt match the one the calculator was initialized on