ClusterSubspace fails on prim derived from CIF file

[dmebane]

heyo -- trying to generate a subspace from a CIF (attached -- .txt extension appended)

"
s = Structure.from_file('Li0.3La0.57TiO3.cif')
prim = s.get_primitive_structure()
subspace = ClusterSubspace.from_cutoffs(prim, cutoffs={2: 1}, basis='indicator', supercell_size='O')
Traceback (most recent call last):

Cell In[21], line 1
subspace = ClusterSubspace.from_cutoffs(prim, cutoffs={2: 1}, basis='indicator', supercell_size='O')

File ~/anaconda3/lib/python3.10/site-packages/smol/cofe/space/clusterspace.py:303 in from_cutoffs
orbits = cls._gen_orbits_from_cutoffs(

File ~/anaconda3/lib/python3.10/site-packages/smol/cofe/space/clusterspace.py:1325 in _gen_orbits_from_cutoffs
site_spaces = get_site_spaces(exp_struct, include_measure=use_conc)

File ~/anaconda3/lib/python3.10/site-packages/smol/cofe/space/domain.py:78 in get_site_spaces
site_space = SiteSpace(

File ~/anaconda3/lib/python3.10/site-packages/smol/cofe/space/domain.py:161 in init
self._data[Vacancy()] = 1 - composition.num_atoms

File ~/anaconda3/lib/python3.10/site-packages/smol/cofe/space/domain.py:262 in init
super().init(

TypeError: DummySpecies.init() got an unexpected keyword argument 'properties'
"

here's the prim for reference:

"
print(prim)
Full Formula (Li1.2 La2.268 Ti4 O12)
Reduced Formula: Li1.2La2.268Ti4O12
abc : 5.505110 5.505110 7.785450
angles: 90.000000 90.000000 90.000000
pbc : True True True
Sites (28)

SP a b c

---

0 Li:0.150 0.108 0.892 0.007
1 Li:0.150 0.608 0.108 0.007
2 Li:0.150 0.392 0.608 0.007
3 Li:0.150 0.892 0.392 0.007
4 Li:0.150 0.892 0.108 0.993
5 Li:0.150 0.392 0.892 0.993
6 Li:0.150 0.608 0.392 0.993
7 Li:0.150 0.108 0.608 0.993
8 La:0.382 0.25 0.75 0
9 La:0.382 0.75 0.25 0
10 La:0.752 0.25 0.75 0.5
11 La:0.752 0.75 0.25 0.5
12 Ti 0.25 0.25 0.2487
13 Ti 0.75 0.75 0.2487
14 Ti 0.75 0.75 0.7513
15 Ti 0.25 0.25 0.7513
16 O 0.5182 0.4818 0.2656
17 O 0.0182 0.5182 0.2656
18 O 0.9818 0.0182 0.2656
19 O 0.4818 0.9818 0.2656
20 O 0.4818 0.5182 0.7344
21 O 0.9818 0.4818 0.7344
22 O 0.0182 0.9818 0.7344
23 O 0.5182 0.0182 0.7344
24 O 0.25 0.25 0
25 O 0.75 0.75 0
26 O 0.25 0.25 0.5
27 O 0.75 0.75 0.5
"

any help / ideas appreciated thank you!

Li0.3La0.57TiO3.cif.txt

[lbluque]

Hi @dmebane, what version of smol and pymatgen are you using?

This is probably related to a recent deprecation of the properties attributed in pymatgen Species.

[dmebane]

aha, ok

smol 0.5.1
pymatgen 2023.9.10

[lbluque]

Ah, that is probably the reason. We have just pushed a fix for this in #412 but I have not made a release. I will aim to create a release with this fix today.

Before then, you can get it to work by installing directly from the repo (instead of PyPI) or downgrading pymatgen.

[dmebane]

sounds great thank you!

[lbluque]

version 0.5.2 which has a fix for this is available on PyPI now.

Feel free to reopen if there are still any related issues.