pymatgen.analysis.prototypes module

This module is intended to match crystal structures against known crystallographic “prototype” structures.

In this module, the AflowPrototypeMatcher uses the AFLOW LIBRARY OF CRYSTALLOGRAPHIC PROTOTYPES. If using this particular class, please cite their publication appropriately:

Mehl, M. J., Hicks, D., Toher, C., Levy, O., Hanson, R. M., Hart, G., & Curtarolo, S. (2017). The AFLOW library of crystallographic prototypes: part 1. Computational Materials Science, 136, S1-S828. https://doi.org/10.1016/j.commatsci.2017.01.017

class AflowPrototypeMatcher(initial_ltol=0.2, initial_stol=0.3, initial_angle_tol=5)[source]

Bases: object

This class will match structures to their crystal prototypes, and will attempt to group species together to match structures derived from prototypes (e.g. an A_xB_1-x_C from a binary prototype), and will give these the names the “-like” suffix.

This class uses data from the AFLOW LIBRARY OF CRYSTALLOGRAPHIC PROTOTYPES. If using this class, please cite their publication appropriately:

Mehl, M. J., Hicks, D., Toher, C., Levy, O., Hanson, R. M., Hart, G., & Curtarolo, S. (2017). The AFLOW library of crystallographic prototypes: part 1. Computational Materials Science, 136, S1-S828. https://doi.org/10.1016/j.commatsci.2017.01.017

Tolerances as defined in StructureMatcher. Tolerances will be gradually decreased until only a single match is found (if possible).

Parameters:

  • initial_ltol – fractional length tolerance

  • initial_stol – site tolerance

  • initial_angle_tol – angle tolerance

get_prototypes(structure)[source]

Get prototype(s) structures for a given input structure. If you use this method in your work, please cite the appropriate AFLOW publication:

Mehl, M. J., Hicks, D., Toher, C., Levy, O., Hanson, R. M., Hart, G., & Curtarolo, S. (2017). The AFLOW library of crystallographic prototypes: part 1. Computational Materials Science, 136, S1-S828. https://doi.org/10.1016/j.commatsci.2017.01.017

Parameters:

structure – structure to match

Returns (list): A list of dicts with keys ‘snl’ for the matched prototype and ‘tags’, a dict of tags (‘mineral’, ‘strukturbericht’ and ‘aflow’) of that prototype. This should be a list containing just a single entry, but it is possible a material can match multiple prototypes.