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If you're using PyNEURON, you have to manually set a NEURONHOME environment variable in order for it to find the HOC libraries. The need for this extra step is unfortunate, but it's a simple process (see, for example, here -- updated 20191029, link broken so removed but this is no longer necessary i...

My sincere apologies. I copied the function out of another file I wrote and didn't test it on its own; it requires the GUI tools to be loaded. I've modified the import accordingly. Please try this version: def instantiate_swc(filename): """load an swc file and instantiate it"&quo...

Yes. Here's a function to load and instantiate a single cell: def instantiate_swc(filename): """load an swc file and instantiate it""" # load the NEURON library (just in case h is defined otherwise elsewhere) from neuron import h # a helper library, included with NEURON...

The exception is critical to the point being discussed. When there is an exception, the local stack frame is not immediately released (and hence variables are not freed), but is preserved in case other code wishes to examine what went wrong. To reproduce the error, copy and paste the code as is into...

The behavior you describe is a property of Python not of NEURON. Here's a NEURON-free example: class A: def __del__(self): print 'obj deleted' def test(): a = A() raise Exception() test() print 'done test' If you run this interactively, it'll print out the error message and then print "done tes...

If you wanted to be super-safe, you could only ever have one copy of a NEURON object (e.g. of a section) that was held by Python and have everything else work with a weakref proxy object. For good measure, you could have the gc module force a garbage collection before any NEURON initialization or ad...

Is the issue that you have no control over the code that is being run? i.e Are you trying to write reusable code (if so, follow Ted's advice)? Or are you trying to run arbitrary simulations whose code you do not control? If it is the latter, are you sure you need it to only be in one process? Why? I...

The main repository now includes your patch. Thanks again.

Thanks. That change makes the API more consistent.

I've added it to my development version of the code.

You're almost there with the part that's not active transport. A few notes: rxd.Species (and rxd.Parameter) work on rxd.Region objects which you can think of as high-level concepts, like: all of the cytosol, all of the ER, etc. The regions argument to rxd.Rate (and rxd.Reaction, etc) currently only ...

One solution is to declare a top-level variable that is used for initialization and set that. For example, consider example.hoc's use of initvalue: // default value for creating new Example objects initvalue = 17 begintemplate Example public value, print_value external initvalue proc print_value() {...

To fix this, you must specify the containing section explicitly with a sec=, as in nc4 = h.NetCon(cell2(0.5)._ref_v,syn_5_2,0,10,0.5, sec=cell2) This is because NEURON needs to know what thread/etc contains the pointer, and this information is not accessible via the raw pointer. As an aside, note th...

Replace the first h.pt3dclear() with h.pt3dclear(sec=soma) and the second with h.pt3dclear(sec=i), then you should be able to remove the "push" calls. The section stack is what provides HOC it's ability to say things like soma { L = 10 nseg = 11 } It's used exactly when something depends o...

Your problem doesn't lie in creating the sections; it lies in "i.push()". You're pushing "i" onto the section stack without ever popping anything from the section stack, so the stack grows and grows. In my opinion, one should never use Section.push. In your specific case, none of...

You are correct; when _currents(rhs) is invoked, rhs already contains the collected currents (ica + ina + ik + etc...), so the current and the voltage derivative (contained in rhs) both must be changed separately. This is because nrn_nonvint_block_current is invoked after nrn_rhs in src/nrnoc/treese...