[Bug]: Fail to parse the element or species on prim cell #475
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bug
Something isn't working
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Thanks for reporting this @ghalibalfaza. I'll have a look at it. I suspect this might be a change in pymatgen. What pymatgen version do you have installed? |
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Dear @ghalibalfaza , thank you for reporting this! I have received several compliants on this issue. I will have a further look when I have time. @kamronald please also take a look at your convenience if possible, thank you! |
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@ghalibalfaza Also as a quick work-around, you may try to install smol from git repo instead of pypi. After cloning the repo to your local machine, try "pip install -r requirements.txt", then "pip install ./" |
4 tasks
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Hi @ghalibalfaza, just found a solution for this in PR #485. Sorry for the delay |
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@kamronald @ghalibalfaza Maybe we can close this issue now? |
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Version
0.5.3
Which OS(es) are you using?
What happened?
I am just following the tutorial but error happened at the third steps. Any help would be greatly appreciated, thanks!
Code snippet
Log output
TypeError Traceback (most recent call last) File ~\AppData\Local\anaconda3\Lib\site-packages\pymatgen\core\periodic_table.py:1534, in get_el_sp(obj) 1533 try: -> 1534 return DummySpecies.from_str(obj) # type: ignore 1535 except Exception: File ~\AppData\Local\anaconda3\Lib\site-packages\pymatgen\core\periodic_table.py:1434, in DummySpecies.from_str(cls, species_string) 1422 """Get a Dummy from a string representation. 1423 1424 Args: (...) 1432 ValueError if species_string cannot be interpreted. 1433 """ -> 1434 if match := re.search(r"([A-ZAa-z]*)([0-9.]*)([+\-]*)(.*)", species_string): 1435 sym = match[1] File ~\AppData\Local\anaconda3\Lib\re\__init__.py:176, in search(pattern, string, flags) 174 """Scan through string looking for a match to the pattern, returning 175 a Match object, or None if no match was found.""" --> 176 return _compile(pattern, flags).search(string) TypeError: expected string or bytes-like object, got 'SiteSpace' During handling of the above exception, another exception occurred: ValueError Traceback (most recent call last) Cell In[3], line 1 ----> 1 subspace = ClusterSubspace.from_cutoffs( 2 lno_prim, 3 cutoffs={2: 5, 3: 4.1}, 4 basis='sinusoid', 5 supercell_size='O2-' 6 ) File ~\AppData\Local\anaconda3\Lib\site-packages\smol\cofe\space\clusterspace.py:303, in ClusterSubspace.from_cutoffs(cls, structure, cutoffs, basis, orthonormal, use_concentration, supercell_matcher, site_matcher, num_threads, **matcher_kwargs) 301 expansion_structure = Structure.from_sites(sites_to_expand) 302 # get orbits within given cutoffs --> 303 orbits = cls._gen_orbits_from_cutoffs( 304 expansion_structure, cutoffs, symops, basis, orthonormal, use_concentration 305 ) 306 return cls( 307 structure=structure, 308 expansion_structure=expansion_structure, (...) 314 **matcher_kwargs, 315 ) File ~\AppData\Local\anaconda3\Lib\site-packages\smol\cofe\space\clusterspace.py:1337, in ClusterSubspace._gen_orbits_from_cutoffs(exp_struct, cutoffs, symops, basis, orthonorm, use_conc) 1334 nbits = np.array([len(b) - 1 for b in site_spaces]) 1336 # Generate singlet/point orbits -> 1337 orbits[1] = ClusterSubspace._gen_point_orbits( 1338 exp_struct, site_bases, nbits, symops 1339 ) 1341 if len(cutoffs) == 0: # return singlets only if no cutoffs provided 1342 return orbits File ~\AppData\Local\anaconda3\Lib\site-packages\smol\cofe\space\clusterspace.py:1373, in ClusterSubspace._gen_point_orbits(exp_struct, site_bases, nbits, symops) 1369 pt_orbits = [] 1370 for nbit, site, sbasis in zip(nbits, exp_struct, site_bases): 1371 # Coordinates of point terms must stay in [0, 1] to guarantee 1372 # correct math of the following algorithm. -> 1373 new_orbit = Orbit( 1374 [np.mod(site.frac_coords, 1)], 1375 exp_struct.lattice, 1376 [list(range(nbit))], 1377 [sbasis], 1378 symops, 1379 ) 1380 if new_orbit not in pt_orbits: 1381 pt_orbits.append(new_orbit) File ~\AppData\Local\anaconda3\Lib\site-packages\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 ~\AppData\Local\anaconda3\Lib\site-packages\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 ~\AppData\Local\anaconda3\Lib\site-packages\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 ~\AppData\Local\anaconda3\Lib\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 ~\AppData\Local\anaconda3\Lib\site-packages\pymatgen\core\periodic_table.py:1536, in get_el_sp(obj) 1534 return DummySpecies.from_str(obj) # type: ignore 1535 except Exception: -> 1536 raise ValueError(f"Can't parse Element or Species from {obj!r}") ValueError: Can't parse Element or Species from Li+0.5 vacA0+0.5 ----Code of Conduct
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