Compute msd of one type of element

Dear all,

Is it possible to calculate the msd of one type of element in perovskites?
I am doing diffusion simulation os SrTiO3, and previously I calculated the three Oxygen atoms msd separately. Now I would like to compute them as a group.
Do appreciate any help.

Thanks,
Zizhen

Screen Shot 2020-07-17 at 8.37.16 am.png

you can define a group that includes all of them, e.g. by using group union.

you can also just post-process the resulting files you already have. that is, you take the average, as that is what the compute will be doing if you combine the groups.

axel.

Screen Shot 2020-07-17 at 8.37.16 am.png

Hi Axel,

Thanks for your advice.
If I want to calculate the time-averaged msd, is it recommended to append “average yes” after the compute command? I read the manual saying it only makes sense whilst atoms are not diffusing. In my system, atoms barely diffuse at low temperature but do diffuse at a higher temperature. Not sure if I can add this average or not.
Or should I process it by myself later?

Regards,
Zizhen

Axel Kohlmeyer <[email protected]> 于2020年7月17日周五 上午8:43写道:

Screen Shot 2020-07-17 at 8.37.16 am.png

that average option is a very different thing from the averaging that i was talking about.

Screen Shot 2020-07-17 at 8.37.16 am.png