Refine structure SpglibDataset error #88
Description
I have installed the latest tdeptools with python3.11 and tried the Fe-hcp example in the documentation in order to refine it. The input given in the documentation is
hcp Fe
2.4
0.50000 -0.866025 0.00000
0.50000 0.866025 0.00000
0.00000 0.000000 1.63299
Fe
2
Direct
0.333333 0.66666 0.25000
0.666666 0.33333 0.75000
The refinement crashed with the following error:
Read 'infile.ucposcar'
... autodetect format vasp for infile.ucposcar
REFINE SYMMETRY w/ SPGLIB
... symprec: 1e-10
... find standardized unitcell https://spglib.readthedocs.io/en/latest/definition.html#spglib-conventions-of-standardized-unit-cell
GEOMETRY INFORMATION FOR RESULTING STRUCTURE
Geometry info
input geometry: Atoms(symbols='Fe2', pbc=True, cell=[[2.399999160749853, 0.0, 0.0], [0.0, 3.9191759999999998, 0.0],
[-1.1999987411246333, 0.0, 2.0784607268118624]])
Symmetry prec.: 1e-10
Number of atoms: 2
Species: Fe (2)
Periodicity: [ True True True]
Positions: x (Å) y (Å) z (Å)
0, 'Fe': 1.800002 2.939382 0.346407
1, 'Fe': -0.600001 0.979794 1.732054
Lattice (Å):
[[ 2.39999916 0. 0. ]
[ 0. 3.919176 0. ]
[-1.19999874 0. 2.07846073]]
Cubicness: 0.459
Largest Cutoff: 1.039 Å
Bounding box rad.: 2.592 Å
Nearest neighbor: 3.394 Å
Cell lengths and angles:
a, b, c (Å): 2.4000 3.9192 2.4000
α, β, γ (°): 90.0000 120.0000 90.0000
Volume: 19.550 Å3
Volume per atom: 9.775 Å3
Report symmetry information from spglib:
/home/vaskarpo/.local/lib/python3.11/site-packages/tdeptools/scripts/ase_geometry_info.py:33: DeprecationWarning: dict interface is deprecated. Use attribute interface instead
uwcks, count = np.unique(dataset["wyckoffs"], return_counts=True)
╭─────────────────────────────────────────────── Traceback (most recent call last) ───────────────────────────────────────────────╮
│ /home/vaskarpo/.local/lib/python3.11/site-packages/tdeptools/scripts/ase_geometry_refine.py:91 in main │
│ │
│ 88 │ │
│ 89 │ echo() │
│ 90 │ echo("GEOMETRY INFORMATION FOR RESULTING STRUCTURE") │
│ ❱ 91 │ inform(atoms, symprec=symprec) │
│ 92 │ │
│ 93 │ echo() │
│ 94 │ echo(f"... save new structure to '{outfile}'") │
│ │
│ /home/vaskarpo/.local/lib/python3.11/site-packages/tdeptools/scripts/ase_geometry_info.py:94 in inform │
│ │
│ 91 │ if symprec is not None: │
│ 92 │ │ echo() │
│ 93 │ │ echo("Report symmetry information from spglib:") │
│ ❱ 94 │ │ sds = get_symmetry_dataset(atoms, symprec=symprec) │
│ 95 │ │ │
│ 96 │ │ echo(f" Spacegroup: {sds.international} ({sds.number})") │
│ 97 │ │ if sds.number > 1: │
│ │
│ /home/vaskarpo/.local/lib/python3.11/site-packages/tdeptools/scripts/ase_geometry_info.py:34 in get_symmetry_dataset │
│ │
│ 31 │ dataset = spg.get_symmetry_dataset(to_spglib_cell(atoms), symprec=symprec) │
│ 32 │ │
│ 33 │ uwcks, count = np.unique(dataset["wyckoffs"], return_counts=True) │
│ ❱ 34 │ dataset["wyckoffs_unique"] = [(w, c) for (w, c) in zip(uwcks, count)] │
│ 35 │ │
│ 36 │ ats, count = np.unique(dataset["equivalent_atoms"], return_counts=True) │
│ 37 │ dataset["equivalent_atoms_unique"] = [(a, c) for (a, c) in zip(ats, count)] │
╰─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
TypeError: 'SpglibDataset' object does not support item assignment
Maybe there is conflict between tdeptools version and python version. Does anyone know if tdeptools works with a specific python version?
Thanks,
Vahid