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I am trying to find symmetrically inequivalent T-atoms in a crystal structure (zeolite). Does anyone happen to know any package that can help with that? I see that pymatgen does have options for symmetry analysis, but I will need some help to understand it. Here is a snippet of the code that I tried on a .cif file, (anyone interested in checking on the cif file, https://europe.iza-structure.org/IZA-SC/mat_cif.php?ID=CHA_0 )

The module from pymatgen, https://pymatgen.org/pymatgen.symmetry.html

import pymatgen.core as pmg
from pymatgen.symmetry.analyzer import cluster_sites
structure = pmg.Structure.from_str(open("./CHA.cif").read(), fmt="cif")
sites = cluster_sites(structure, tol=0.1)

The output is,

(None,
 defaultdict(list,
             {(4.99070644043773,
               Comp: Si1): [PeriodicSite: Si (8.2387, 1.1508, 5.5161) [0.8954, 0.1241, 0.6673], PeriodicSite: Si (5.5368, 8.3047, 0.0694) [0.6673, 0.8954, 0.1241], PeriodicSite: Si (0.6537, 6.1886, 7.8040) [0.1241, 0.6673, 0.8954], PeriodicSite: Si (0.4825, 8.3047, 5.5161) [0.1241, 0.8954, 0.6673], PeriodicSite: Si (7.8310, 6.1886, 0.0694) [0.8954, 0.6673, 0.1241], PeriodicSite: Si (6.1157, 1.1508, 7.8040) [0.6673, 0.1241, 0.8954]],
              (4.255705851873808,
               Comp: Si1): [PeriodicSite: Si (8.0719, 0.9699, 2.4219) [0.8759, 0.1046, 0.3327], PeriodicSite: Si (0.7234, 3.0860, 7.8686) [0.1046, 0.3327, 0.8759], PeriodicSite: Si (2.4387, 8.1238, 0.1340) [0.3327, 0.8759, 0.1046], PeriodicSite: Si (0.3157, 8.1238, 2.4219) [0.1046, 0.8759, 0.3327], PeriodicSite: Si (3.0176, 0.9699, 7.8686) [0.3327, 0.1046, 0.8759], PeriodicSite: Si (7.9007, 3.0860, 0.1340) [0.8759, 0.3327, 0.1046]],
              (4.721664892674799,
               Comp: O1): [PeriodicSite: O (6.8820, 1.0159, 6.3861) [0.7484, 0.1095, 0.7484], PeriodicSite: O (6.4025, 6.9415, -0.0205) [0.7484, 0.7484, 0.1095], PeriodicSite: O (0.4574, 6.9415, 6.3861) [0.1095, 0.7484, 0.7484]],
              (4.255705851873808,
               Comp: O1): [PeriodicSite: O (8.0970, 2.3331, 1.5519) [0.8905, 0.2516, 0.2516], PeriodicSite: O (2.1519, 2.3331, 7.9586) [0.2516, 0.2516, 0.8905], PeriodicSite: O (1.6724, 8.2588, 1.5519) [0.2516, 0.8905, 0.2516]],
              (6.650526506176671,
               Comp: O1): [PeriodicSite: O (8.5779, 6.3230, 7.9598) [0.9768, 0.6818, 0.9768], PeriodicSite: O (8.3564, 9.0599, 5.0007) [0.9768, 0.9768, 0.6818], PeriodicSite: O (5.6105, 9.0599, 7.9598) [0.6818, 0.9768, 0.9768]],
              (1.4759151389461997,
               Comp: O1): [PeriodicSite: O (2.9439, 0.2147, -0.0218) [0.3182, 0.0232, 0.0232], PeriodicSite: O (0.1980, 0.2147, 2.9373) [0.0232, 0.0232, 0.3182], PeriodicSite: O (-0.0235, 2.9517, -0.0218) [0.0232, 0.3182, 0.0232]],
              (3.5640104664911534,
               Comp: O1): [PeriodicSite: O (6.8592, 0.0000, 1.9392) [0.7371, 0.0000, 0.2629], PeriodicSite: O (1.8925, 6.8368, -0.6965) [0.2629, 0.7371, 0.0000], PeriodicSite: O (-0.1973, 2.4378, 6.6953) [0.0000, 0.2629, 0.7371], PeriodicSite: O (2.4458, 0.0000, 6.6953) [0.2628, 0.0000, 0.7371], PeriodicSite: O (6.6619, 2.4378, -0.6965) [0.7371, 0.2628, 0.0000], PeriodicSite: O (-0.5533, 6.8368, 1.9392) [0.0000, 0.7371, 0.2628]],
              (4.438228227072944,
               Comp: O1): [PeriodicSite: O (7.5563, 4.6373, 0.4353) [0.8524, 0.5000, 0.1476], PeriodicSite: O (0.7336, 7.9057, 3.9690) [0.1476, 0.8524, 0.5000], PeriodicSite: O (4.5417, 1.3689, 7.5027) [0.5000, 0.1476, 0.8524], PeriodicSite: O (0.9981, 4.6373, 7.5027) [0.1476, 0.5000, 0.8524], PeriodicSite: O (7.8208, 1.3689, 3.9690) [0.8524, 0.1476, 0.5000], PeriodicSite: O (4.0127, 7.9057, 0.4353) [0.5000, 0.8524, 0.1476]]}))

I used on the zeolite structure called CHA for which there exists one type of T-atom (Si- atom), check below, enter image description here

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1 Answer 1

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I guess that T refers to 'tetrahedral'; this site is occupied by Si and Al. In the cif file these atoms have exactly the same coordinates because Al substitutes Si. So you have one single T site randomly occupied by both Si and Al.

The Wyckoff notation for this site is 36i, where 36 indicates the number of this site in the unit-cell. It is the site with the highest multiplicity in the space group R-3m; this means that the only symmetry operation to be considered is the identity.

Anyway, I checked the original paper; it seems to me that these data (Table 3) are not properly reported. There's no correspondence between the names of Wyckoff sites (it is written 12i instead of 36i, for example), and the relationships among coordinates do not comply with those reported in the International Table of Crystallography vol A. I would use other data.

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