Hello Guys
I am studying the diffusion behaviour in the SiC, since the code calculate the diffusion coefficient by calculating the MSD, I am wondering does the LAMMPS calculate the avg MSD for all atoms in the super cell or the most prominent one (e.g. around defect) ?
In any case I am searching for the MSD solely around vacancy as i am interested in the vacancy diffusion behaviour can anyone help how ic an narrow my search of msd only around diffusing vacancy ?
KR
Irslan Ullah Ashraf
LAMMPS computes the MSD as average over all atoms in the compute group.
I don’t think that a direct MSD computation is a good choice for the kind of analysis you want to do.
There are many discussions in the archive where I have explained that diffusion computed from MSD for atoms with geometrical restrictions is not well defined and can easily lead to biased output.
If you want to study the diffusion of the vacancies, you will have to figure out a way to define a “vacancy trajectory” (and specifically also consider what happens, if two vacancies merge or one bigger vacancy splits into two small ones). From that you can try to quantify the diffusivity. Typically, all of this would be done as a post-processing step. I am not aware of any feature in LAMMPS that would automate the process (since it can be very system specific).
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