Dear Lammps developers:
I am using compute voronoi/atom to detect vacancies and interstitials in my system. However, besides the number of vacancies and interstitials in the system, I also want to know their positions in the reference frame (first invocation). Is there a simple way to output this information? Or can you give me some suggestions where to start if I need to modify the compute_voronoi_atom.cpp file? Thank you very much!
Shijun
The position of an interstitial is an atom coord. If you
know which atom is an interstitial, then you have its
position. If you can infer an interstitial from its
local volume (compute voronoi), then you can output it.
E.g. do a dump of atom coords, with a dump_modify thresh
condition on the output of compute voronoi/atom.
How do you define the position
of a vacancy? Not clear how LAMMPS would know
the position of an atom that isn’t there.
Steve
Thank you very much.
Yes, that is my question. So I mean I’d like to output their positions in the reference frame (initial configurations). In this frame, both vacancy and interstitial have definitive coordinates.
For now, I know lammps can output current positions, but I want to know their positions in the first step.
Is there a way to do that?
Thanks.
The position of an interstitial is an atom coord. If you
know which atom is an interstitial, then you have its
position. If you can infer an interstitial from its
local volume (compute voronoi), then you can output it.
E.g. do a dump of atom coords, with a dump_modify thresh
condition on the output of compute voronoi/atom.
How do you define the position
of a vacancy? Not clear how LAMMPS would know
the position of an atom that isn’t there.
Steve
Fix store/state will store coord (or other per-atom properties)
at some initial time and carry them around with each atom.
You can access those coords in a dump command if you like
to output them.
Steve