example fail

[jsyony37]

Hello,

I'm running one of the examples. It fails at this line:

prim = loadfn('lno_prim.json')
empty_cutoff = {} # Defining the cut-offs as an empty dictionary will generate a subspace with empty cluster
subspace = ClusterSubspace.from_cutoffs(
    structure=prim, cutoffs=empty_cutoff, supercell_size='O2-'
)

but it fails with the error traced back to
ValueError: Can't parse Element or Species from Li+0.5 vacA0+0.5

What could be wrong here?

The full error message is pasted below:

---

TypeError                                 Traceback (most recent call last)
File ~/miniconda3/lib/python3.9/site-packages/pymatgen/core/periodic_table.py:1659, in get_el_sp(obj)
   1658 try:
-> 1659     return DummySpecies.from_str(obj)  # type: ignore[arg-type]
   1660 except Exception as exc:

File ~/miniconda3/lib/python3.9/site-packages/pymatgen/core/periodic_table.py:1550, in DummySpecies.from_str(cls, species_string)
   1538 """Get a Dummy from a string representation.
   1539 
   1540 Args:
   (...)
   1548     ValueError if species_string cannot be interpreted.
   1549 """
-> 1550 if match := re.search(r"([A-ZAa-z]*)([0-9.]*)([+\-]*)(.*)", species_string):
   1551     sym = match[1]

File ~/miniconda3/lib/python3.9/re.py:201, in search(pattern, string, flags)
    199 """Scan through string looking for a match to the pattern, returning
    200 a Match object, or None if no match was found."""
--> 201 return _compile(pattern, flags).search(string)

TypeError: expected string or bytes-like object

The above exception was the direct cause of the following exception:

ValueError                                Traceback (most recent call last)
Cell In[3], line 3
      1 hi = loadfn('/Users/cpark21/Downloads/lno_prim.json')
      2 empty_cutoff = {} # Defining the cut-offs as an empty dictionary will generate a subspace with empty cluster
----> 3 subspace = ClusterSubspace.from_cutoffs(
      4     structure=hi, cutoffs=empty_cutoff, supercell_size='O2-'
      5 )

File ~/tools/smol/smol/cofe/space/clusterspace.py:304, in ClusterSubspace.from_cutoffs(cls, structure, cutoffs, basis, orthonormal, use_concentration, supercell_matcher, site_matcher, num_threads, **matcher_kwargs)
    302 print(expansion_structure)
    303 # get orbits within given cutoffs
--> 304 orbits = cls._gen_orbits_from_cutoffs(
    305     expansion_structure, cutoffs, symops, basis, orthonormal, use_concentration
    306 )
    307 return cls(
    308     structure=structure,
    309     expansion_structure=expansion_structure,
   (...)
    315     **matcher_kwargs,
    316 )

File ~/tools/smol/smol/cofe/space/clusterspace.py:1338, in ClusterSubspace._gen_orbits_from_cutoffs(exp_struct, cutoffs, symops, basis, orthonorm, use_conc)
   1335 nbits = np.array([len(b) - 1 for b in site_spaces])
   1337 # Generate singlet/point orbits
-> 1338 orbits[1] = ClusterSubspace._gen_point_orbits(
   1339     exp_struct, site_bases, nbits, symops
   1340 )
   1342 if len(cutoffs) == 0:  # return singlets only if no cutoffs provided
   1343     return orbits

File ~/tools/smol/smol/cofe/space/clusterspace.py:1374, in ClusterSubspace._gen_point_orbits(exp_struct, site_bases, nbits, symops)
   1370 pt_orbits = []
   1371 for nbit, site, sbasis in zip(nbits, exp_struct, site_bases):
   1372     # Coordinates of point terms must stay in [0, 1] to guarantee
   1373     # correct math of the following algorithm.
-> 1374     new_orbit = Orbit(
   1375         [np.mod(site.frac_coords, 1)],
   1376         exp_struct.lattice,
   1377         [list(range(nbit))],
   1378         [sbasis],
   1379         symops,
   1380     )
   1381     if new_orbit not in pt_orbits:
   1382         pt_orbits.append(new_orbit)

File ~/tools/smol/smol/cofe/space/orbit.py:106, in Orbit.__init__(self, cluster_coords, lattice, bits, site_bases, structure_symops)
    103 self._flat_corr_tensors = None
    105 # Create basecluster
--> 106 self.base_cluster = Cluster(
    107     [site_basis.site_space for site_basis in site_bases],
    108     cluster_coords,
    109     lattice,
    110 )

File ~/tools/smol/smol/cofe/space/cluster.py:60, in Cluster.__init__(self, site_spaces, frac_coords, lattice)
     58 self._centroid = centroid - shift
     59 self._frac_coords = frac_coords - shift
---> 60 self._sites = tuple(
     61     Site(site_space, coords)
     62     for site_space, coords in zip(
     63         site_spaces, lattice.get_cartesian_coords(frac_coords)
     64     )
     65 )
     66 self._lattice = lattice
     67 self.id = None

File ~/tools/smol/smol/cofe/space/cluster.py:61, in <genexpr>(.0)
     58 self._centroid = centroid - shift
     59 self._frac_coords = frac_coords - shift
     60 self._sites = tuple(
---> 61     Site(site_space, coords)
     62     for site_space, coords in zip(
     63         site_spaces, lattice.get_cartesian_coords(frac_coords)
     64     )
     65 )
     66 self._lattice = lattice
     67 self.id = None

File ~/miniconda3/lib/python3.9/site-packages/pymatgen/core/sites.py:66, in Site.__init__(self, species, coords, properties, label, skip_checks)
     64 if not isinstance(species, Composition):
     65     try:
---> 66         species = Composition({get_el_sp(species): 1})  # type: ignore[arg-type]
     67     except TypeError:
     68         species = Composition(species)

File ~/miniconda3/lib/python3.9/site-packages/pymatgen/core/periodic_table.py:1661, in get_el_sp(obj)
   1659     return DummySpecies.from_str(obj)  # type: ignore[arg-type]
   1660 except Exception as exc:
-> 1661     raise ValueError(f"Can't parse Element or Species from {obj!r}") from exc

ValueError: Can't parse Element or Species from Li+0.5 vacA0+0.5

[jsyony37]

Found the answer in one of the issues raised.