[ase-users] another nearest neighbor list question

[John Kitchin]

hurray! it works! Thanks for fixing that.

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





2011/2/21 Jens Jørgen Mortensen <jensj at fysik.dtu.dk>:
> 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
>> >> _______________________________________________
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>> >> ase-users at listserv.fysik.dtu.dk
>> >> https://listserv.fysik.dtu.dk/mailman/listinfo/ase-users
>> >
>> >
>>
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>
>