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lamalab-org / xtal2txt

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extract local environments #50

Closed kjappelbaum closed 2 months ago

kjappelbaum commented 3 months ago

using smth like 

from pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies import SimplestChemenvStrategy
from pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder import LocalGeometryFinder
from pymatgen.analysis.chemenv.coordination_environments.structure_environments import LightStructureEnvironments
from pymatgen.analysis.chemenv.connectivity.connectivity_finder import ConnectivityFinder
from pymatgen.analysis.chemenv.connectivity.structure_connectivity import StructureConnectivity

strategy = SimplestChemenvStrategy()

lgf = LocalGeometryFinder() 

lgf.setup_structure(structure = structure)

se = lgf.compute_structure_environments(
    only_cations          = True,
    valences              = oxid_states,
    additional_conditions = additional_conditions)

lse = LightStructureEnvironments.from_structure_environments(
    strategy               = strategy,
    structure_environments = se)

cf = ConnectivityFinder()
sc = cf.get_structure_connectivity(light_structure_environments = lse)