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Posted: **Mon May 12, 2025 5:16 pm**

Hello,

I am working on a model of the granular layer in which Golgi and granule cells are explicitly modelled.
I would like to add the 3D location of each cell using pt3dadd. I am able to do so for the Golgi cells. However, when adding the 3D location to the granule cells' soma, the job crashes with the following error:

Code: Select all

NEURON: spFactor error: Singular
  in run.hoc near line 776
  pc1.psolve(tstop)
            ^     
      ParallelContext[0].psolve(20)
     xopen("run.hoc")

Adding the location itself does not produce an error, the job crashes when the model is being run. Also, the model runs fine when the 3D location of the granule cells is not defined.

I would appreciate any help on how to debug this.

Thank you,
Kind regards

Posted: **Tue May 13, 2025 11:49 am**

I seem to have misplaced my scrying stone, and without that it is difficult to diagnose the unseen. Perhaps you could share what you mean by "add the 3D location" e.g. by providing code examples of what you did that worked, and what you did that didn't work.

Posted: **Sun Jun 01, 2025 5:19 pm**

Hi Ted,

Thank you for offering to look at my code. I tried reproducing the issue with the simplest model possible, but I didn't manage to. In the end I decided not to add the locations to the cells.

Posted: **Tue Jun 03, 2025 11:43 am**

You might find a solution to your problem by reading about specification of geometry with Python
https://nrn.readthedocs.io/en/latest/py ... y-geometry
or hoc
https://nrn.readthedocs.io/en/latest/ho ... l#geometry

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Simulation fails when adding 3D location to cell

Simulation fails when adding 3D location to cell

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