Comments (5)
JaGeo
commented on June 11, 2024
Thanks for raising the issue.
Could you be a bit more specific on the output that you get? For example, if you are using the cation-anion modus in the analysis, I would expect the anion neighbor lists to be empty.
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Atefeh-Yadegarifard
commented on June 11, 2024
Hello. I am using all the default settings of the ChemEnv module. This error also occurs for cations. For example in the code below, ChemEnv shows an empty list for the site 2, which is Na atom:
from pymatgen.core.structure import Structure
from pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder import LocalGeometryFinder
from pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies import SimplestChemenvStrategy, MultiWeightsChemenvStrategy
from pymatgen.analysis.chemenv.coordination_environments.structure_environments import LightStructureEnvironments
cif_file='030a7f2455.CIF'
structure = Structure.from_file (cif_file)
lgf = LocalGeometryFinder()
lgf.setup_parameters(centering_type="centroid", include_central_site_in_centroid=True)
lgf.setup_structure(structure=structure)
se = lgf.compute_structure_environments(maximum_distance_factor=1.41)
strategy = MultiWeightsChemenvStrategy.stats_article_weights_parameters()
lse = LightStructureEnvironments.from_structure_environments(strategy=strategy, structure_environments=se)
species = {}
for i in range(len(lse.as_dict()['structure']['sites'])):
species[i] = (lse.as_dict()['structure']['sites'][i]['label'])
print (species)
print (lse.coordination_environments[2])
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JaGeo
commented on June 11, 2024
Will need to check in more detail.
My ideas:
- remove "maximum_distance_factor" to see what happens
- check what happens if you look at all bonds instead of cation-anion ones.
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JaGeo
commented on June 11, 2024
If you provide the valences with the bond valence analyser, everything works as expected:
from pymatgen.core.structure import Structure
from pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder import LocalGeometryFinder
from pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies import SimplestChemenvStrategy, \
MultiWeightsChemenvStrategy
from pymatgen.analysis.chemenv.coordination_environments.structure_environments import LightStructureEnvironments
from pymatgen.analysis.bond_valence import BVAnalyzer
cif_file = '030a7f2455.CIF'
structure = Structure.from_file(cif_file)
bva = BVAnalyzer()
valences = bva.get_valences(structure)
lgf = LocalGeometryFinder()
lgf.setup_structure(structure=structure)
se = lgf.compute_structure_environments(valences=valences)
strategy = MultiWeightsChemenvStrategy.stats_article_weights_parameters()
lse = LightStructureEnvironments.from_structure_environments(strategy=strategy, structure_environments=se)
for isite, (site,ce) in enumerate(zip(structure, lse.coordination_environments)):
if ce is not None:
print(site.species_string+str(isite)+': '+str(ce[0]["ce_symbol"]))ChemEnv cannot deal with coordination numbers larger 13. The coordination numbers get larger 13 if you consider all bonds.
Output from the code above is:
Na0: DDPN:8
Na1: DDPN:8
Na2: BO_2:8
Na3: T:6
Na4: BO_2:8
Na5: DDPN:8
Na6: T:6
Na7: DDPN:8
Na8: T:6
Na9: BO_2:8
Na10: BO_2:8
Na11: T:6
Eu12: SBT:8
Eu13: SBT:8
Eu14: SBT:8
Eu15: SBT:8
B16: TL:3
B17: TL:3
B18: TL:3
B19: TL:3
B20: TL:3
B21: TL:3
B22: TL:3
B23: TL:3
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JaGeo
commented on June 11, 2024
I think it is resolved. I am therefore closing the issue. Let me know if there are further issues.
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