[ase-users] Inconsistent space group determination for ICSD_CollCode262928.cif

[Hongyi Zhao]

Dear ASE community,

I've encountered an interesting case of space group determination
inconsistency using ASE for the structure ICSD_CollCode262928.cif.
Here are the details:

The ase version:

(datasci) werner at x13dai-t:~$ pip list |grep ^ase
ase                           3.23.0

The test is as follows:

```python
In [15]: import numpy as np
    ...: from ase.io import read
    ...: from ase.spacegroup import get_spacegroup
    ...:
    ...: def analyze_space_group_ase(filename):
    ...:     """Analyze space group using ASE with different tolerances."""
    ...:     # Read the CIF file
    ...:     atoms = read(filename)
    ...:
    ...:     # Define tolerances to test
    ...:     tolerances = [1e-1, 1e-2, 1e-3, 1e-4, 1e-5, 1e-6, 1e-7]
    ...:
    ...:     print(f"Analysis for file: {filename}")
    ...:     print(f"Cell parameters:\n{atoms.cell}")
    ...:     print(f"Number of atoms: {len(atoms)}")
    ...:     print(f"Atom types: {set(atoms.get_chemical_symbols())}")
    ...:
    ...:     for tol in tolerances:
    ...:         spacegroup = get_spacegroup(atoms, symprec=tol)
    ...:         print(f"Tolerance {tol:.1e}: {spacegroup.symbol}
({spacegroup.no})")
    ...:
    ...: if __name__ == "__main__":
    ...:     cif_file = "ICSD_CollCode262928.cif"
    ...:     analyze_space_group_ase(cif_file)
    ...:
Analysis for file: ICSD_CollCode262928.cif
Cell parameters:
Cell([[3.3717, 0.0, 0.0], [-1.6858499999999994, 2.9199778539399923,
0.0], [0.0, 0.0, 5.3855]])
Number of atoms: 4
Atom types: {'Mn', 'O'}
Tolerance 1.0e-01: P 63 m c (186)
Tolerance 1.0e-02: P 63 m c (186)
Tolerance 1.0e-03: P 63 m c (186)
Tolerance 1.0e-04: P 63 m c (186)
Tolerance 1.0e-05: C m c 21 (36)
Tolerance 1.0e-06: C m c 21 (36)
Tolerance 1.0e-07: C m c 21 (36)
```

As you can see:

1. Structure Information:
   - File: ICSD_CollCode262928.cif
   - Cell parameters:
     [[3.3717, 0.0, 0.0],
      [-1.6858499999999994, 2.9199778539399923, 0.0],
      [0.0, 0.0, 5.3855]]
   - Number of atoms: 4
   - Atom types: Mn, O

2. Space group determination results using different tolerances:
   - 1.0e-01 to 1.0e-04: P 63 m c (186)
   - 1.0e-05 to 1.0e-07: C m c 21 (36)

This structure shows a transition in the determined space group when
the tolerance is changed from 1.0e-04 to 1.0e-05.

Questions:
1. Is this behavior expected?
2. Which space group should be considered as the "correct" one for
this structure?
3. Are there any recommendations for handling such cases where the
space group determination is sensitive to the tolerance value?

I would appreciate any insights or explanations about this behavior,
as well as best practices for reporting space groups in such
borderline cases.

Thank you for your time and expertise.

Best regards,
Zhao
-- 
Assoc. Prof. Hongsheng Zhao <hongyi.zhao at gmail.com>
Theory and Simulation of Materials
Hebei Vocational University of Technology and Engineering
No. 473, Quannan West Street, Xindu District, Xingtai, Hebei province
-------------- next part --------------
A non-text attachment was scrubbed...
Name: ICSD_CollCode262928.cif.zip
Type: application/zip
Size: 1072 bytes
Desc: not available
URL: <http://listserv.fysik.dtu.dk/pipermail/ase-users/attachments/20240729/82c1de22/attachment.zip>