data.oc.utils.flag_anomaly#
Copyright (c) Meta Platforms, Inc. and affiliates.
This source code is licensed under the MIT license found in the LICENSE file in the root directory of this source tree.
Classes#
Module Contents#
- class data.oc.utils.flag_anomaly.DetectTrajAnomaly(init_atoms, final_atoms, atoms_tag, final_slab_atoms=None, surface_change_cutoff_multiplier=1.5, desorption_cutoff_multiplier=1.5)#
- init_atoms#
- final_atoms#
- final_slab_atoms#
- atoms_tag#
- surface_change_cutoff_multiplier#
- desorption_cutoff_multiplier#
- is_adsorbate_dissociated()#
Tests if the initial adsorbate connectivity is maintained.
- Returns:
True if the connectivity was not maintained, otherwise False
- Return type:
(bool)
- has_surface_changed()#
Tests bond breaking / forming events within a tolerance on the surface so that systems with significant adsorbate induces surface changes may be discarded since the reference to the relaxed slab may no longer be valid.
- Returns:
True if the surface is reconstructed, otherwise False
- Return type:
(bool)
- is_adsorbate_desorbed()#
If the adsorbate binding atoms have no connection with slab atoms, consider it desorbed.
- Returns:
True if there is desorption, otherwise False
- Return type:
(bool)
- _get_connectivity(atoms, cutoff_multiplier=1.0)#
Generate the connectivity of an atoms obj.
- Parameters:
atoms (ase.Atoms) – object which will have its connectivity considered
cutoff_multiplier (float, optional) – cushion for small atom movements when assessing atom connectivity
- Returns:
The connectivity matrix of the atoms object.
- Return type:
(np.ndarray)
- is_adsorbate_intercalated()#
Ensure the adsorbate isn’t interacting with an atom that is not allowed to relax.
- Returns:
True if any adsorbate atom neighbors a frozen atom, otherwise False
- Return type:
(bool)