[Wien] Regarding Local environments of individual atom in a structure

[pieper]

High Sandeep,

I think this has not been answered, so I will give it a try:

Yes, case.outputnn would be one place to look for information about 
local environments. By way of an example I copied a few lines from 
case.outputnn of a Co hcp structure. The lines starting with % are 
comments I inserted

...
  ATOM:  1  EQUIV.  1  Co         AT   0.33333   0.66667   0.25000
% Specifies the environment of which atom is listed in the following 
lines.
% Position in crystal coordinates.
  RMT(  1)=2.34000 AND RMT(  1)=2.34000
% RMT of that atom (there are 2 Co per unit cell) and of a nearest 
neighbor
  SUMS TO 4.68000  LT.  NN-DIST= 4.71810
% nearest neighbor distance must be greater than sum of RMT's
  ATOM:  1  Co        AT -0.3333  0.3333 -0.2500 IS  4.71810 A.U.   
2.49671 ANG
% Position in crystal coordinates of the first nearest neighbor,
& and distance in a.u. and Angstrom
  ATOM:  1  Co        AT -0.3333  0.3333  0.7500 IS  4.71810 A.U.   
2.49671 ANG
% The same for the second nearest neighbor
  ATOM:  1  Co        AT  0.6667  1.3333 -0.2500 IS  4.71810 A.U.   
2.49671 ANG
  ATOM:  1  Co        AT  0.6667  1.3333  0.7500 IS  4.71810 A.U.   
2.49671 ANG
  ATOM:  1  Co        AT  0.6667  0.3333 -0.2500 IS  4.71810 A.U.   
2.49671 ANG
  ATOM:  1  Co        AT  0.6667  0.3333  0.7500 IS  4.71810 A.U.   
2.49671 ANG
% There are 6 nearest neighbors in the hcp structure, all at the same 
distance.
  ATOM:  1  Co        AT  1.3333  0.6667  0.2500 IS  4.73773 A.U.   
2.50710 ANG
% Position in crystal coordinates and distance
% of the first next nearest neighbor atom
...

There are also 6 next nearest neighbors in this case, which are listed 
in the following lines. If you need further shells set the associated 
call parameter for nn to higher values (see user guide).

If you need (binding) angles you can calculate them from the position 
data (remember to transform to cartesian coordinates), or use your 
favorite crystal structure viewer (xcrysden works fine).

Take information about local symmetry from case.outputs (or 
case.outputsgroup). In case.outputs you will find for each atom in 
case.struct a list of symmetry elements for that position. For atom 1 in 
th above case of hcp-Co this reads:

...
  ATOM:           1
Co         operation #  1     1
Co         operation #  4     2 || 120
Co         operation #  5     2 || 210
Co         operation #  6     2 || 1-10
Co         operation # 14     m (s-h) n  z
Co         operation # 18     m (s-v)  n  100
Co         operation # 19     m (s-v)  n  010
Co         operation # 20     m (s-v)  n  110
Co         operation # 21     3 || z
Co         operation # 22     3 || -z
Co         operation # 23     S3 (-6) || z
Co         operation # 24     S3 (-6) || -z
% There is identity, three 2-fold axes, four mirror planes,
%two 3-fold axes (along +/-z), and two 6-fold screw axes
   pointgroup is -6m2 (neg. iatnr!!)
% The point group with these symmetry elements
   axes should be: -6 || z, m n y
   z-rotation vector:  0.0000  0.0000  1.0000
   y-rotation vector:  0.0000  1.0000  0.0000    2
% Orientation of the local axes, highest symmetry along z
%(here 6-fold rotation), next along y (mirror plane normal y)
   WARNING: LOCAL ROTATION MATRIX CHANGED
LOCAL ROT MATRIX:       NEW                                OLD
            1.0000000 0.0000000 0.0000000      0.0000000 0.0000000 
0.0000000
            0.0000000 1.0000000 0.0000000      0.0000000 0.0000000 
0.0000000
            0.0000000 0.0000000 1.0000000      0.0000000 0.0000000 
0.0000000
% Local rotation matrices belonging to this orientation (see user guide)
...

I hope this helps. Best regards,

Martin Pieper



---
Dr. Martin Pieper
Karl-Franzens University
Institute of Physics
Universitätsplatz 5
A-8010 Graz
Austria
Tel.: +43-(0)316-380-8564


Am 18.09.2018 12:34, schrieb sandeep Kumar:
> Dear Prof. Peter Blaha and WIEN2k Users,
> 
> I am trying to find the local environments of an individual atom in a
> structure. In VASP code, it is written clearly in the OUTCAR file that
> how many atoms and which atom are nearest neighbour around an
> individual atom in a structure. We can also analysis local
> environments from the structure itself using VESTA.
> 
> Can we do in the WIEN2k code using case.outputnn file ? Could you
> please explain it to me?
> 
> Thanks
> 
> Sandeep
> 
> --
> 
> Dr. Sandeep Kumar (Postdoctoral Research Fellow)
> Institute for Nanotechnology & Advanced Materials,
> Department of Chemistry,
> Bar-Ilan University, Ramat-Gan 52900, Israel
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