Bug fixing, code and text improving

Created by: didi-hou

This PR fixed the problem of computing the firing rate over all areas instead of only all simulated areas. Besides, it reorganized the structure of the notebook, and refined plots, texts, and comments.

• It corrected the bug that the firing rate in plots was computed from all areas, instead now it is computed from only the simulated populations
• It reorganized the structure of the notebook and enhanced the plots, texts, and comments
• It removed the unnecessary file VERSION_LOG.md
• It removed the plot of instantaneous and mean firing rate and added only printing the mean firing rate of all simulated populations