[ase-users] NeighborList radii

Jens Jørgen Mortensen jensj at fysik.dtu.dk
Wed May 7 11:29:04 CEST 2014


Den 05-05-2014 19:13, Peterson, Andrew skrev:
> Hi,
>
> I was confused with the NeighborList module giving unexpected results, 
> until I came across this note from a 2008 message by JJ:
>
> http://listserv.fysik.dtu.dk/pipermail/ase-users/2008-November/000104.html
> A small "skin" will be added to the radii (default value is skin=0.3 Å),
> so the effective cutoff is 1.75 Å.  All atoms within a distance of 3.5 Å
> from the C atom are therefore counted as neighbors, and that is all
> atoms except number 9.
> If the effective cutoff is 1.75 Angstroms, then shouldn't atoms only 
> within a distance of 1.75 Angstroms from the central atom be counted 
> as neighbors? This seems like the definition of a cutoff radius to me. 
> Why is this being doubled to 3.5? Am I missing something in the 
> nomenclature?

You give each atom a radius that will define a sphere for each atom.  
Then neighbors of an atom will be those spheres that overlap with the 
sphere of that atom.  Maybe we should rename the "cutoffs" argument to 
"radii" - would that help?

Jens Jørgen

> thanks,
> Andy
>
> -- 
> Andrew Peterson
> Assistant Professor
> Brown University School of Engineering
> Barus & Holley 247
> 184 Hope Street
> Providence, RI 02912
> (401) 863-2153
> http://brown.edu/go/catalyst
>
>
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