Interpreting the Mode of Operation

Suppose you are inspecting a simulation, to see what it does and how it does it. You know hsolve is being used in the simulation, but you do not know where in the scripts it is configured. This short section will help you out. The first step is to locate all hsolve elements:

  genesis > echo {el /##[][TYPE=hsolve]}
  /purkinje

Then for every hsolve element reported, you inspect the chanmode, calcmode and path field.

  genesis > showfield /purkinje path chanmode calcmode
  [ /purkinje ]
  path                 = ./##[][TYPE=compartment]
  chanmode             = 4
  calcmode             = 1

The path field tells you that all compartments below the hsolve element have been taken over by /purkinje. The chanmode is four which means that also all intracellular mechanisms within the compartments will be computed by hsolve. Finally the calcmode tells that all tables are used with linear interpolation to compute results.

The numerical method that hsolve uses for the cable equations and the equations of intracellular mechanisms is found with the following command:

  genesis > showfield /purkinje object->method
  [ /purkinje ]
  object->method       = 11

So in this case Crank-Nicolson is used to update the variables.