pymatgen.analysis.structure_prediction.substitution_probability module

This module provides classes for representing species substitution probabilities.

class SubstitutionPredictor(lambda_table=None, alpha=-5, threshold=0.001)

Bases: object

Predicts likely substitutions either to or from a given composition or species list using the SubstitutionProbability

Parameters:

• () (lambda_table) – Input lambda table.

• alpha (float) – weight function for never observed substitutions

• threshold (float) – Threshold to use to identify high probability structures.

composition_prediction(composition, to_this_composition=True)

Returns charged balanced substitutions from a starting or ending composition.

Parameters:

• composition – starting or ending composition

• to_this_composition – If true, substitutions with this as a final composition will be found. If false, substitutions with this as a starting composition will be found (these are slightly different)

Returns:

List of predictions in the form of dictionaries. If to_this_composition is true, the values of the dictionary will be from the list species. If false, the keys will be from that list.

list_prediction(species, to_this_composition=True)

Parameters:

• species – list of species

• to_this_composition – If true, substitutions with this as a final composition will be found. If false, substitutions with this as a starting composition will be found (these are slightly different)

Returns:

List of predictions in the form of dictionaries. If to_this_composition is true, the values of the dictionary will be from the list species. If false, the keys will be from that list.

class SubstitutionProbability(*args, **kwargs)

Bases: SubstitutionProbability

This class finds substitution probabilities given lists of atoms to substitute. The inputs make more sense if you look through the from_defaults static method.

The substitution prediction algorithm is presented in: Hautier, G., Fischer, C., Ehrlacher, V., Jain, A., and Ceder, G. (2011) Data Mined Ionic Substitutions for the Discovery of New Compounds. Inorganic Chemistry, 50(2), 656-663. doi:10.1021/ic102031h

Parameters:

• lambda_table – json table of the weight functions lambda if None, will use the default lambda.json table

• alpha – weight function for never observed substitutions