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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?
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