poreana.diffusion

Analyse diffusion in a pore.

Bin Method

bins(link[, ax_area, is_norm])	This function calculates the axial (z-axis) diffusion coefficient as a function of the radial distance.
bins_plot(data[, intent, kwargs])	This function calculates the axial plots the diffusion profile calculated by the function poreana.diffusion.bins().
cui(link[, z_dist, ax_area, intent, is_fit, …])	This function samples and calculates the diffusion coefficient of a molecule group in a pore in both axial and radial direction, as described in the paper of Cui.
mean(diff_data, dens_data[, ax_area, is_print])	This function uses the diffusion coefficient slope obtained from

MC Method

mc_fit(link[, len_step, section, is_std, …])	This function uses the diffusion profiles over box length which are calculated in the function poreana.mc.MC.run() to estimate the final diffusion coefficient.
mc_profile(link[, len_step, section, …])	This function plots the diffusion profile for an infinity lag time (\(\Delta t_{\alpha} \rightarrow \infty\)) over the box fitted with the specified \(\mathrm{len}\_\mathrm{step}\) list.
mc_trans_mat(link, step[, kwargs, is_norm, …])	This function plots the occupation of a normalized transition matrix as a heatmap.