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To fix, add the following two paths to your system PATH environment variable (for instructions on how to modify PATH, see https://www.architectryan.com/2018/03/17/add-to-the-path-on-windows-10/ ): c:\nrn\bin c:\nrn\mingw\usr\bin We've identified the source of the 1024 limit, and this should be fixed...

This is likely due to a previously under-appreciated detail in the numerical methods used for 3D simulation. In particular, we use scipy.sparse.linalg.bicgstab with a tolerance of 1e-5 to solve a matrix problem. This should have been connected to the atol used elsewhere*, but it is not. For now, you...

Adaptive integration chooses timesteps to constrain error.

In particular, unlike fixed step integration, it will adapt its timesteps to handle events at the time received and not shift them or group them.

Conceptually, you are correct. For memory reasons, however, NEURON's hh.mod doesn't actually store those values since they are only useful for computing one location at one time point. Instead, a GLOBAL value is used, meaning that there is only one memory location used for every spatial point (diffe...

Globals are accessed globally; i.e. through the h object:

What's happening is that NEURON currently assumes a limit on ion name lengths. You can see this without rxd in that the following two lines will crash NEURON: from neuron import h h.ion_register('x'*50, 0) If, as in your example code, you have a pure reaction-diffusion model (no ion channels) you ca...

Since this discussion, there had been a lot of work on the Python interface to make things cleaner, especially in NEURON 7.5 and 7.6. We're in the process of reworking the main NEURON Python tutorial: https://neuron.yale.edu/neuron/static/docs/neuronpython/index.html The draft revised pages (only th...

I suggest trying the following to get NEURON to work:

Download and install the .deb from http://neuron.yale.edu

Then (to allow both Anaconda and your system Python to find NEURON) add the following to your ~/.bashrc:

Strictly speaking, the command on the installer's line 13 sudo apt install -y python3-pyqt5 python3-pip python3-pyqtgraph python3-opengl zlib1g-dev zlib1g zlibc libx11-dev mercurial bison flex automake libtool libxext-dev libncurses-dev python3-dev xfonts-100dpi cython libopenmpi-dev python3-scipy p...

The bad news: The reaction-diffusion module rxd currently only directly supports reactions and diffusions. So you could add arbitrary local kinetics, but you'd have to modify the source to add the type of dynamics you describe. The good news: besides storing parameters, all of the changes would be c...

There is some discussion about how segment areas and volumes are calculated at: https://www.neuron.yale.edu/neuron/static/py_doc/modelspec/programmatic/topology/geometry.html#d-specification-of-geometry To say what hines said another way: in your first case, you're defining a tapered shape while the...

Most likely that means that either Python is not installed, or it is installed but NEURON can't connect to it (likely a path issue). You're free to program NEURON models in HOC or Python, but to use the rxd module, Python must be installed and loadable by NEURON To check for this, check the return v...

Are you using a fixed time step or variable? I assume variable step will choose time points at the beginning and end of each current change... And thus you would see the current injection having an effect. If fixed, what is dt? Note that for fixed step, the default timestep (0.025 ms) is longer than...

Doesn't solve the mystery, but...

Assuming the morphology is not changing with successive runs, you could load it once before entering the loop, and see this particular issue entirely

You can probably do what you want by using Vector.play . In brief, Vector.play allows you to use two Vectors (one listing time points and one with the values) to control an arbitrary memory location (e.g. a current, or in your case a variable in a MOD file). Example that plays a stimulus into the in...