This is the README file for running simulations associated with:

Newton, A.J.H, McDougal, R.A., Hines, M.L. and Lytton, W.W., 2018. Using NEURON
for reaction-diffusion modeling of extracellular dynamics. Frontiers in
neuroinformatics, 12.

This code was contributed by AJH Newton and questions should be addressed to

There are two examples included here, the trivial example used for validations
(figure 4) and the spreading depression simulation (figures 1 and 2).

Run, it will display the plot shown in figure 4 (with dx = 1) and
create a 'trivial_1.00.npy' file with the results. To get the other relative
errors shown in 4C modify the dx parameter (line 19). accepts command line arguments to switch between the 4
different model combinations. To run it first compile the NEURON mod files. An
error in the original model where multiple dendrite segments were used has been
 corrected leading to quantitatively but not qualitatively different results
from those report in the paper. 

usage: [-h] [--edema] [--buffer] [--tstop [TSTOP]] dir

Run the spreading depression simulation

positional arguments:
  dir              a directory to save the figures and data

optional arguments:
  -h, --help       show this help message and exit
  --edema          Use inhomogeneous tortuosity and volume fraction to
                   simulate edema
  --buffer         Use a reaction to model astrocytic buffering
  --tstop [TSTOP]  duration of the simulation in ms (defaults to 200ms)

The spreading depression simulations are computationally demanding, a demo
version with fewer larger neurons and larger extracellular voxels is included