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rad-identify-wannier-centres#

Identifies wannier centres with respect to the atom or to the point between the atom`s pair.

Changed in version 0.6: Renamed from identify-wannier-centres.py

Changed in version 0.9.0: Renamed from rad-identify-wannier-centres.py to rad-identify-wannier-centres

Use --span option to increase the distance span for the search.

  • If the centre is associated with some atom

    then -> atom appears in the output file.

  • If the centre is unidentified

    then -> None appears in the output file and additional information is present in the console and in the output file.

Usage example#

Example is based on the files from examples folder.

The "example_centres.xyz" file looks like this:

    28
 Wannier centres, written by Wannier90 on16Sep2022 at 12:23:35
X          2.70102543       1.20456455       1.74829100
X          2.70102543       1.20456455       1.73136237
X          2.70102542       1.20456454       1.71844477
X          2.70102540       1.20456454       1.74850456
X          2.70102542       1.20456455       1.74171453
X          0.90034180       3.61369365       3.82242305
X          0.90034181       3.61369365       3.83936190
X          0.90034181       3.61369365       3.85226490
X          0.90034182       3.61369365       3.82220340
X          0.90034181       3.61369365       3.82899496
X          2.70102543       3.61369365       2.21721708
X          2.70102542       3.61369367       2.29147179
X          2.70102540       3.61369365       2.17808141
X          0.90034181       1.20456453       3.35355250
X          0.90034181       1.20456457       3.27930790
X          0.90034180       1.20456458       3.39269417
X          0.90034181       1.20456455      -0.05695451
X          0.90034182       1.20456455       0.02140611
X          0.90034181       1.20456456      -0.04741017
X          2.70102542       3.61369365       5.62773652
X          2.70102542       3.61369366       5.54938336
X          2.70102542       3.61369365       5.61819448
Br         0.90034179       1.20456453      -0.07878122
Br         2.70102536       3.61369358       5.64955786
Cr         2.70102536       1.20456453       1.73263498
Cr         0.90034179       3.61369358       3.83807392
S          2.70102536       3.61369358       2.20990738
S          0.90034179       1.20456453       3.36085407

Lets run the code:

rad-identify-wannier-centres -if example_centres.xyz

This command creates an output file "example_centre.xyz_identified" in the directory of the input file with the following content:

    28
 Wannier centres, written by Wannier90 on16Sep2022 at 12:23:35
X          2.70102543       1.20456455       1.74829100   ->   Cr1
X          2.70102543       1.20456455       1.73136237   ->   Cr1
X          2.70102542       1.20456454       1.71844477   ->   Cr1
X          2.70102540       1.20456454       1.74850456   ->   Cr1
X          2.70102542       1.20456455       1.74171453   ->   Cr1
X          0.90034180       3.61369365       3.82242305   ->   Cr2
X          0.90034181       3.61369365       3.83936190   ->   Cr2
X          0.90034181       3.61369365       3.85226490   ->   Cr2
X          0.90034182       3.61369365       3.82220340   ->   Cr2
X          0.90034181       3.61369365       3.82899496   ->   Cr2
X          2.70102543       3.61369365       2.21721708   ->   S1
X          2.70102542       3.61369367       2.29147179   ->   S1
X          2.70102540       3.61369365       2.17808141   ->   S1
X          0.90034181       1.20456453       3.35355250   ->   S2
X          0.90034181       1.20456457       3.27930790   ->   S2
X          0.90034180       1.20456458       3.39269417   ->   S2
X          0.90034181       1.20456455      -0.05695451   ->   Br1
X          0.90034182       1.20456455       0.02140611   ->   None, closest: Br1 (0.10018733)
X          0.90034181       1.20456456      -0.04741017   ->   Br1
X          2.70102542       3.61369365       5.62773652   ->   Br2
X          2.70102542       3.61369366       5.54938336   ->   None, closest: Br2 (0.10017450)
X          2.70102542       3.61369365       5.61819448   ->   Br2
Br         0.90034179       1.20456453      -0.07878122   ->   Br1
Br         2.70102536       3.61369358       5.64955786   ->   Br2
Cr         2.70102536       1.20456453       1.73263498   ->   Cr1
Cr         0.90034179       3.61369358       3.83807392   ->   Cr2
S          2.70102536       3.61369358       2.20990738   ->   S1
S          0.90034179       1.20456453       3.36085407   ->   S2

which means that two centres are not identified. The script provides the distance to the closest atom for each unidentified centre. In the output file some information about unidentified centres is provided as well.

As one can see first unidentified centre is quite close to the \(\text{Br}_1\) and the second one to the \(\text{Br}_2\), let us extend the span a little bit in order to correctly identify all the atoms:

rad-identify-wannier-centres -if example_centres.xyz --span 0.11 --output-name example_centres.xyz_bigger_span

This command produces example_centres.xyz_bigger_span file:

    28
 Wannier centres, written by Wannier90 on16Sep2022 at 12:23:35
X          2.70102543       1.20456455       1.74829100   ->   Cr1
X          2.70102543       1.20456455       1.73136237   ->   Cr1
X          2.70102542       1.20456454       1.71844477   ->   Cr1
X          2.70102540       1.20456454       1.74850456   ->   Cr1
X          2.70102542       1.20456455       1.74171453   ->   Cr1
X          0.90034180       3.61369365       3.82242305   ->   Cr2
X          0.90034181       3.61369365       3.83936190   ->   Cr2
X          0.90034181       3.61369365       3.85226490   ->   Cr2
X          0.90034182       3.61369365       3.82220340   ->   Cr2
X          0.90034181       3.61369365       3.82899496   ->   Cr2
X          2.70102543       3.61369365       2.21721708   ->   S1
X          2.70102542       3.61369367       2.29147179   ->   S1
X          2.70102540       3.61369365       2.17808141   ->   S1
X          0.90034181       1.20456453       3.35355250   ->   S2
X          0.90034181       1.20456457       3.27930790   ->   S2
X          0.90034180       1.20456458       3.39269417   ->   S2
X          0.90034181       1.20456455      -0.05695451   ->   Br1
X          0.90034182       1.20456455       0.02140611   ->   Br1
X          0.90034181       1.20456456      -0.04741017   ->   Br1
X          2.70102542       3.61369365       5.62773652   ->   Br2
X          2.70102542       3.61369366       5.54938336   ->   Br2
X          2.70102542       3.61369365       5.61819448   ->   Br2
Br         0.90034179       1.20456453      -0.07878122   ->   Br1
Br         2.70102536       3.61369358       5.64955786   ->   Br2
Cr         2.70102536       1.20456453       1.73263498   ->   Cr1
Cr         0.90034179       3.61369358       3.83807392   ->   Cr2
S          2.70102536       3.61369358       2.20990738   ->   S1
S          0.90034179       1.20456453       3.36085407   ->   S2

where all centres are correctly identified.

Hint

Set span to 0 to see the distances to the closest atom in the output file for each wannier center.

Arguments#

-if, --input-filename#

Relative or absolute path to the "_centres.xyz" file

Identified Wannier centres are stored in the "filename_identified" file.

required
type: str

Changed in version 0.8.0: Renamed from filename

-s, --span#

Distance tolerance between centre and atom. (in Angstroms)

If some centres remain unidentified try to increase the span.

default: 0.1
type: float

-on, --output-name#

Seedname for the output files.

See also: example

default: ""
type: str