leetmaa
Question about cutoff in CustomRateCalculator
I am trying to apply KMCLib on diffusion problem within a hexagonal lattice.
I want the diffusion rate to be calculated from nearest neighbor atoms so I tried CustomRateCalculator.
As there seems to be no explicit nearest neighbor list so I thought that defining cutoff might work.
However the cutoff is seems to be like:
The distance D between a site and the center is calculated as
D = sqrt(x^2 + y^2 + z^2)
where (x,y,z) is the internal coordinate of the site.
Only the sites with D < cutoff will be counted.
So cutoff only works when the lattice is a cubic with a = b = c.
Since I have a hexagonal lattice, in which, for example, the distance between (0,0,0) and (1,1,0) is just the same as that between (0,0,0) and (1,0,0), while setting cutoff to 1 just includes (1,0,0) but excludes (1,1,0).
Is there any way to define cutoff as an absolute distance?
As you have noticed the cutoff is set in primitive cell internal coordinates. I think your best option is to go for a larger cutoff and ignore some of the extra sites you'll inevitable get in the neighbor geometry when you do the rate calculation.
It's been some time now since you asked the question. Did you find a way forward?
