changing units in mod files for NEURON

Question

How to change units in a mod file so that after running neuoConstract the units will be saved?

units:  0.001 sec
units:  1
The units of the previous two expressions are not conformable
 at line 75 in file C:/Users/miria/Desktop/neuro/neuroConstruct_1.7.2/nCexamples/Ex4_HHcell/generatedNEURON/CurrentClampExt.mod
            beginNextCycle = beginNextCycle + (del + dur)<<ERROR>>

I have tried to change with Notepad++ but the changes can not be saved for the next time.

Answer 1

The error that you are getting here is the result of unit mismatch between the RHS and LHS of the equation:

beginNextCycle = beginNextCycle + (del + dur)

in CurrentClampExt.mod file. beginNextCycle, del and dur should have the same units e.g. millisecond.

For editing the CurrentClampExt.mod file, you can use Notepad++ or any other text editor. The constants/variables for equation are declared most likely in the mod file's ASSIGNED or PARAMETER block. Make sure that the these variables follow a unit. For example:

ASSIGNED {
          dur (ms)
          del (ms)
}

where (ms) refers to millisecond.

You can check the units of mod files by using NEURON simulator's 'modlunit' feature. See here for more details: https://www.neuron.yale.edu/neuron/static/docs/nmodl/mswin.html

Once you are done with unit correction, then compile the mod file(s) using nrnivmodl (as shown in the above link). If there are no errors, then try to run the code using neuroConstruct.