how to calculate Na diffusion coefficient in Si bulk

[nadeemqasr]

I am very new user to ATK and especially beginner to DFT studies. Could anyone please suggest me tutorial or example to calculate the diffusion coefficient for a case when Na ion diffuses into Sn bulk crystal structure? I have heard about NEB method and MD simulation but not know how to do that. Any response will be appreciated.

[nadeemqasr]

Actually i can see a tutorial that tells how to calculate the barrier that barrier is required for diffusion calculations. Here is the problem that i do not know how to do that. I have seen some papers who use some kind of mean square displacement (r) and simulation time (t) etc. I can share these text or papers.
please do guide me details if anyone knows.

[zh]

When you do the MD simulation of your system, you save the trajectory (i.e., the  atomic coordinates) of every MD simulation step (or, every several MD stimulation steps) and then calculate the mean square displacement from these trajectory.  In the last step, you have to do a bit but easy coding. If you can't do it, you may find available tools from internet:
http://www.pages.drexel.edu/~cfa22/msim/node29.html
http://www.multiscalelab.org/utilities/DiffusionCoefficientTool
https://nanohub.org/resources/22854
http://www.mdanalysis.org/

[nadeemqasr]

I am very thankful for your reply. I am now practicing the KMC/MD simulations for trajectory save. and meanwhile studying the links you provided. Just in case,could you please tell me how to save the trajactory (.nc) file to vasp DATACAR file? or other formats to see the details of positions during the diffusion?

[zh]

The ATK already provides a class for calculating the mean-square-displacement from an MD trajectory and an example for the diffusion cofficient:
http://www.quantumwise.com/documents/manuals/latest/ReferenceManual/index.html/ref.meansquaredisplacement.html