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1) You can reduce the number of nodes by changing dx. Also nthreads is only currently implemented for crxd extracellular reaction-diffusion. Would a radial diffusion model be sufficient? Radial diffusion can be implemented in rxd using multicompartment reactions, for example; from neuron import h, c...

Here's a working version of your code: from neuron import h, rxd from matplotlib import pyplot # needed for standard run system h.load_file('stdrun.hoc') left = h.Section(name='left') right = h.Section(name='right') left.nseg = right.nseg = 101 left.L = right.L = 101 right.connect(left) tfact0 = 137...

There are several ways of changing the initial concentration of a species, but the easiest is to use its `.initial` attribute, e.g. from neuron import h, rxd soma = h.Section('soma') cyt = rxd.Region([soma], name='cyt', nrn_region='i') ca = rxd.Species(cyt, name='ca', charge=2, initial=50e-6) # firs...

If python is install nrniv should find it.

Try installing the latest version of NEURON from the website https://neuron.yale.edu/neuron/download, the installer has the option to set the correct paths for you.

Python must be installed to use rxd and is the prefered interface for specifying new models. If you are working with an existing model created in hoc, there are three ways you could include rxd in the simulation. 1] The simplest way is to specify rxd in python and load it in your hoc file with `nrnp...

Hi,

Sorry to hear that. Could you provide a minimal example of the code that is producing different results? Also how do the results differ?

Thanks.

I was not able to reproduce the error using the current release NEURON 7.5 or development version NEURON 7.6 https://github.com/neuronsimulator/nrn . We may have already fixed this bug. Could you try running the following code; #Additional code from neuron import h, rxd h.load_file('stdrun.hoc') sec...

To set inhomogeneous initial concentrations you can use a function which take an rxd.Node as an argument. Node has several properties; including x (the 1D location), sec, region and segment. If you want the buffers to diffusion between the spine and dendrite you should use the same region. Here is a...

Sorry for the delay in responding. You can use NMODL for the reactions pathway and link the output to rxd using node.include_flux, as in the example you linked to; https://senselab.med.yale.edu/ModelDB/ShowModel.cshtml?model=185858&file=/CaHDemo/onepyr.py#tabs-2 (see the setmGLURflux function). ...

Hi, We are extending the reaction-diffusion module (rxd) to support extracellular space, it’s not currently implement in the distributed version of NEURON, but the source code is available on github https://github.com/ramcdougal/nrn.git Here is a simple example of two cells in the extracellular spac...