poreana.diffusion.
bins
(link, ax_area=[0.2, 0.8], is_norm=False)¶This function calculates the axial (z-axis) diffusion coefficient as a function of the radial distance. This is done by sampling the mean square displacement for all molecules in a radial sub volume.
The mean square displacement is sampled in function
poreana.sample.Sample._diffusion_bin()
.
For each bin, the msd is summed up, resulting into a msd slope for each bin. Thus, the axial diffusion coefficient can be calculated using
Note that the msd is evaluated in the area, where the slope is uniform, which means that the first twenty and last twenty percent should be neglected.
If is_norm
is set to True, the radius will be normalized in respect
to the effective radius which means, the last radius that has a
Diffusion greater than zero is taken
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