How to use the atoml.fingerprint.adsorbate_prep.autogen_info function in atoml

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github SUNCAT-Center / CatKit / docs / tutorials / 9_adsorbate_fingerprints.py View on Github external
# Usually, the chemical formula (Hill) is available for the adsorbate.
    # It will be used by AtoML if attached like so:
    slab.info['key_value_pairs'] = {}
    slab.info['key_value_pairs']['species'] = ads
    # If the adsorbate consist of the same elements that the slab does,
    # it is preferable to specify the atomic indices belonging to the adsorbate.
    slab.info['ads_atoms'] = [12]
    # Append them to a list.
    images.append(slab)

# If you import from an ase.db, it is recommended to make use of
    # atoml.api.ase_atoms_api.database_to_list

# Some information is expected to be attached to atoms objects.
#   There are various ways of doing this, but the easiest is to call
AtoML_atoms = autogen_info(images)
# This is where checks should be made

# Instantiate the fingerprint generator for adsorbate structures.
fingerprinter = FeatureGenerator()

# All user methods under the fingerprinter accepts an atoms object and
#   returns a vector.
functions = [fingerprinter.mean_chemisorbed_atoms,
             fingerprinter.count_chemisorbed_fragment,
             fingerprinter.count_ads_atoms,
             fingerprinter.count_ads_bonds,
             fingerprinter.ads_av,
             fingerprinter.ads_sum,
             fingerprinter.bulk,
             fingerprinter.term,
             fingerprinter.strain,

atoml

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