[ase-users] another nearest neighbor list question

[Jens Jørgen Mortensen]

On Thu, 2011-02-17 at 10:19 -0500, John Kitchin wrote:
> That doesn't make sense to me. There are 12 atoms that are equidistant
> from the origin. The halflist shouldn't apply or change the results of
> this case because there is only one atom in the unit cell.
> 
> If I make a 3x3x3 bulk fcc cell,  and get the neighbor list of the
> central atom, then it returns only 8 atoms even with bothways=True. I
> would have expected 12 atoms.

Yes, you should get 12.  Fixed in trunk.

Jens Jørgen

> John
> 
> -----------------------------------
> John Kitchin
> Assistant Professor
> Doherty Hall A207F
> Department of Chemical Engineering
> Carnegie Mellon University
> Pittsburgh, PA 15213
> 412-268-7803
> http://kitchingroup.cheme.cmu.edu
> 
> 
> 
> 
> 
> On Thu, Feb 17, 2011 at 9:49 AM, Tao Jiang <tjiang at fysik.dtu.dk> wrote:
> > I think this is the half list as Jakob mentioned before. By doing so,
> > the calculator such as emt does not need to go through the whole
> > list twice to calculate the total energy.
> >
> > /TJ
> >
> >
> > On Feb 17, 2011, at 3:25 PM, John Kitchin wrote:
> >
> >> for the nearest neighbor list, would you expect to get 12 results for
> >> the atom at the origin of an FCC bulk lattice (not counting the atom
> >> itself)? I only get 6 neighbors. Am I misunderstanding the results, or
> >> how to setup the list?
> >>
> >> from ase.lattice.cubic import FaceCenteredCubic
> >> from ase.calculators.neighborlist import *
> >>
> >> atoms = FaceCenteredCubic(directions=[[0,1,1], [1,0,1], [1,1,0]],
> >>                          size=(1,1,1), symbol='Cu', pbc=(1,1,1))
> >>
> >>
> >> nl = NeighborList([2.6/2.],bothways=False,self_interaction=False)
> >> nl.update(atoms)
> >> indices, offsets = nl.get_neighbors(0)
> >>
> >> print indices
> >> print offsets
> >>
> >> [0 0 0 0 0 0]
> >> [[ 0  0  1]
> >> [ 0  1 -1]
> >> [ 0  1  0]
> >> [ 1 -1  0]
> >> [ 1  0 -1]
> >> [ 1  0  0]]
> >>
> >>
> >> John
> >>
> >> -----------------------------------
> >> John Kitchin
> >> Assistant Professor
> >> Doherty Hall A207F
> >> Department of Chemical Engineering
> >> Carnegie Mellon University
> >> Pittsburgh, PA 15213
> >> 412-268-7803
> >> http://kitchingroup.cheme.cmu.edu
> >> _______________________________________________
> >> ase-users mailing list
> >> ase-users at listserv.fysik.dtu.dk
> >> https://listserv.fysik.dtu.dk/mailman/listinfo/ase-users
> >
> >
> 
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