catkit.gen.analysis package¶
Submodules¶
catkit.gen.analysis.classifier module¶
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class
catkit.gen.analysis.classifier.
Classifier
(atoms)[source]¶ Class for classification of various aspects of an an atomic unit cell.
Currently, a tool for classification of adsorbates on surface environments and the active sites they rest on.
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id_adsorbate_atoms
(classifier='trivial', tag=False)[source]¶ Identify adsorbed atoms in a given atoms object.
Parameters: Returns: ads_atoms – Index of adsorbate atoms found.
Return type: ndarray (n,)
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id_adsorbates
(classifier='radial', return_atoms=False)[source]¶ Return a list of Gratoms objects for each adsorbate classified on a surface. Requires classification of adsorbate atoms.
Parameters: Returns: adsorbates – Adsorbate indices of adsorbates in unit cell.
Return type: list (n,)
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id_slab_atoms
(classifier='trivial', tag=False, rtol=0.001)[source]¶ Return the indices of the slab atoms using select characterization techniques.
Parameters: Returns: slab_atoms – Index of slab atoms found.
Return type: ndarray (n,)
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id_surface_atoms
(classifier='voronoi_sweep')[source]¶ Identify surface atoms of an atoms object. This will require that adsorbate atoms have already been identified.
Parameters: classifier (str) – Classification technique to identify surface atoms.
’voronoi_sweep’: Create a sweep of proxy atoms above surface. Surface atoms are those which are most frequent neighbors of the sweep.
Returns: surface_atoms – Index of the surface atoms in the object. Return type: ndarray (n,)
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catkit.gen.analysis.matching module¶
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catkit.gen.analysis.matching.
reactant_indices
(R1, R2, P, broken_bond)[source]¶ - Match the indices of a pair of reactants from a
- product and broken bond.
Parameters: - R1 (networkx MultiGraph) – Graph representing reactant 1
- R2 (networkx MultiGraph) – Graph representing reactant 2
- P (networkx MultiGraph) – Graph representing the product
- broken_bond (list (2,)) – Indices representing the edge of the product to be removed.
Returns: pindex – Indices of the product graph sorted by the order of the reactants indices.
Return type: ndarrays (n,)
catkit.gen.analysis.reconfiguration module¶
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catkit.gen.analysis.reconfiguration.
id_reconstruction
(images, save=False)[source]¶ Identify a reconstruction event by analyzing changes in the forces.
Parameters: - images (list of ASE atoms objects) – Relaxation trajectory.
- show (bool) – Create a figure to display the events located.
Returns: predicted_events – index of images predicted before the event occurs.
Return type: list of int
Module contents¶
-
class
catkit.gen.analysis.
Classifier
(atoms)[source]¶ Class for classification of various aspects of an an atomic unit cell.
Currently, a tool for classification of adsorbates on surface environments and the active sites they rest on.
-
id_adsorbate_atoms
(classifier='trivial', tag=False)[source]¶ Identify adsorbed atoms in a given atoms object.
Parameters: Returns: ads_atoms – Index of adsorbate atoms found.
Return type: ndarray (n,)
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id_adsorbates
(classifier='radial', return_atoms=False)[source]¶ Return a list of Gratoms objects for each adsorbate classified on a surface. Requires classification of adsorbate atoms.
Parameters: Returns: adsorbates – Adsorbate indices of adsorbates in unit cell.
Return type: list (n,)
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id_slab_atoms
(classifier='trivial', tag=False, rtol=0.001)[source]¶ Return the indices of the slab atoms using select characterization techniques.
Parameters: Returns: slab_atoms – Index of slab atoms found.
Return type: ndarray (n,)
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id_surface_atoms
(classifier='voronoi_sweep')[source]¶ Identify surface atoms of an atoms object. This will require that adsorbate atoms have already been identified.
Parameters: classifier (str) – Classification technique to identify surface atoms.
’voronoi_sweep’: Create a sweep of proxy atoms above surface. Surface atoms are those which are most frequent neighbors of the sweep.
Returns: surface_atoms – Index of the surface atoms in the object. Return type: ndarray (n,)
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