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add matbench_discovery/structure/prototype.py module for generating A…
…FLOW-style protostructure labels - replace aviary's get_protostructure_label_from_spglib with matbench_discovery.structure.prototype.get_protostructure_label in data/mp/get_mp_energies.py and data/wbm/compile_wbm_test_set.py - add test cases for prototype structure labeling - update 2023-01-10 mp-energies.csv.gz with moyo-based prototype labels (~50k out of 154k still missing where label generation failed so also keeping the original spglib labels for now)
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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| """Get AFLOW prototype labels for crystal structures using Moyopy for symmetry | ||
| detection. | ||
| """ | ||
|
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| import gzip | ||
| import itertools | ||
| import math | ||
| import os | ||
| import string | ||
| from typing import Final | ||
|
|
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| import moyopy | ||
| import yaml | ||
| from pymatgen.core import Composition, Structure | ||
|
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| __author__ = "Janosh Riebesell" | ||
| __date__ = "2022-12-02" | ||
|
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| module_dir = os.path.dirname(__file__) | ||
|
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| with gzip.open( | ||
| f"{module_dir}/wyckoff-position-multiplicities.yaml.gz", "rb" | ||
| ) as gz_file: | ||
| wyckoff_multiplicity_dict = yaml.safe_load(gz_file) | ||
|
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| with gzip.open(f"{module_dir}/wyckoff-position-relabelings.yaml.gz") as gz_file: | ||
| wyckoff_relabelings = yaml.safe_load(gz_file) | ||
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| crys_sys_letters: Final[dict[str, str]] = { | ||
| "Triclinic": "a", | ||
| "Monoclinic": "m", | ||
| "Orthorhombic": "o", | ||
| "Tetragonal": "t", | ||
| "Trigonal": "h", | ||
| "Hexagonal": "h", | ||
| "Cubic": "c", | ||
| } | ||
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| def get_pearson_symbol(moyo_data: moyopy.MoyoDataset) -> str: | ||
| """Get the Pearson symbol for the structure from a MoyoDataset.""" | ||
| hall_entry = moyopy.HallSymbolEntry(hall_number=moyo_data.hall_number) | ||
| spg_sym = hall_entry.hm_short | ||
| # Get centering from first letter of space group symbol, handle special case for | ||
| # C-centered | ||
| centering = "C" if spg_sym[0] in ("A", "B", "C", "S") else spg_sym[0] | ||
| n_sites = len(moyo_data.std_cell.numbers) | ||
| crys_sys = str(moyo_data.crystal_system) | ||
| return f"{crys_sys_letters[crys_sys]}{centering}{n_sites}" | ||
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| def get_prototype_formula(composition: Composition, amt_tol: float = 1e-8) -> str: | ||
| """Get anonymized formula for a Composition where species are in alphabetical | ||
| order and assigned ascending letters. This format is used in the Aflow | ||
| structure prototype labelling scheme. | ||
| Args: | ||
| composition (Composition): Pymatgen Composition to process | ||
| amt_tol (float): Tolerance for amount of species. Defaults to 1e-8. | ||
| Returns: | ||
| str: anonymized formula where the species are in alphabetical order | ||
| """ | ||
| reduced = composition.element_composition | ||
| if all(x == int(x) for x in composition.values()): | ||
| gcd = math.gcd(*map(int, composition.values())) | ||
| reduced /= gcd | ||
|
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||
| return "".join( | ||
| f"{elem}{int(amt) if abs(amt % 1) < amt_tol else amt}" if amt != 1 else elem | ||
| for elem, amt in zip( | ||
| string.ascii_uppercase, | ||
| [reduced[key] for key in sorted(reduced, key=str)], | ||
| ) | ||
| ) | ||
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| def canonicalize_wyckoffs(element_wyckoffs: str, spg_num: int) -> str: | ||
| """Given an element ordering, canonicalize the associated Wyckoff positions | ||
| based on the alphabetical weight of equivalent choices of origin. | ||
| Args: | ||
| element_wyckoffs (str): wyckoff substring section from aflow_label with the | ||
| wyckoff letters for different elements separated by underscores. | ||
| spg_num (int | str): International space group number. | ||
| Returns: | ||
| str: element_wyckoff string with canonical ordering of the wyckoff letters. | ||
| """ | ||
| scored_wyckoffs: list[tuple[str, int]] = [] | ||
|
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| for trans in wyckoff_relabelings[spg_num]: | ||
| wyckoffs = element_wyckoffs.translate(str.maketrans(trans)) | ||
| score: int = 0 | ||
| sorted_wyckoffs: list[str] = [] | ||
|
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| for el_wyckoff_letter in wyckoffs.split("_"): | ||
| # Split into alpha and numeric groups | ||
| groups = [ | ||
| "".join(grp) | ||
| for _, grp in itertools.groupby(el_wyckoff_letter, str.isalpha) | ||
| ] | ||
| letters = [char for char in groups if char.isalpha()] | ||
| counts = [char for char in groups if char.isnumeric()] | ||
|
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| # Sort by Wyckoff letter and build string | ||
| sorted_pairs = sorted(zip(counts, letters), key=lambda x: x[1]) | ||
| sorted_wyckoffs.append( | ||
| "".join( | ||
| f"{count}{letter}" if count != "1" else letter | ||
| for count, letter in sorted_pairs | ||
| ) | ||
| ) | ||
| score += sum(0 if letter == "A" else ord(letter) - 96 for letter in letters) | ||
|
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| scored_wyckoffs += [("_".join(sorted_wyckoffs), score)] | ||
|
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| return min(scored_wyckoffs, key=lambda x: (x[1], x[0]))[0] | ||
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| def get_protostructure_label( | ||
| struct: Structure, *, symprec: float = 0.1, raise_errors: bool = False | ||
| ) -> str | None: | ||
| """Get AFLOW-style proto-structure label using Moyopy for symmetry detection. | ||
| Args: | ||
| struct (Structure): pymatgen Structure object. | ||
| symprec (float): Initial symmetry precision for Moyopy. Defaults to 0.1. | ||
| raise_errors (bool): Whether to raise ValueError for failing structures or | ||
| return the error message as string instead of the prototype label. Defaults | ||
| to False. | ||
| Returns: | ||
| str: protostructure_label which is constructed as `aflow_label:chemsys` or | ||
| explanation of failure if symmetry detection failed and `raise_errors` | ||
| is False. | ||
| """ | ||
| import moyopy.interface | ||
|
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||
| moyo_cell = moyopy.interface.MoyoAdapter.from_structure(struct) | ||
| symmetry_data = moyopy.MoyoDataset(moyo_cell, symprec=symprec) | ||
| spg_num = symmetry_data.number | ||
|
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| # Group sites by orbit | ||
| orbit_groups: list[list[int]] = [] | ||
| current_orbit: list[int] = [] | ||
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| for idx, orbit_id in enumerate(symmetry_data.orbits): | ||
| if not current_orbit or orbit_id == symmetry_data.orbits[current_orbit[0]]: | ||
| current_orbit += [idx] | ||
| else: | ||
| orbit_groups += [current_orbit] | ||
| current_orbit = [idx] | ||
| if current_orbit: | ||
| orbit_groups += [current_orbit] | ||
|
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| # Create equivalent_wyckoff_labels from orbit groups | ||
| element_dict: dict[str, int] = {} | ||
| element_wyckoffs: list[str] = [] | ||
|
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| equivalent_wyckoff_labels = [ | ||
| ( | ||
| struct.species[orbit[0]].symbol, | ||
| len(orbit), | ||
| symmetry_data.wyckoffs[orbit[0]].translate( | ||
| str.maketrans("", "", string.digits) | ||
| ), | ||
| ) | ||
| for orbit in orbit_groups | ||
| ] | ||
| equivalent_wyckoff_labels = sorted( | ||
| equivalent_wyckoff_labels, key=lambda x: (x[0], x[2]) | ||
| ) | ||
|
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||
| for el, group in itertools.groupby(equivalent_wyckoff_labels, key=lambda x: x[0]): | ||
| # NOTE create a list from the iterator so that we can use it without exhausting | ||
| label_group = list(group) | ||
| element_dict[el] = sum( | ||
| wyckoff_multiplicity_dict[spg_num][itm[2]] for itm in label_group | ||
| ) | ||
| wyckoff_counts_str = "".join( | ||
| f"{len(list(occurrences))}{wyk_letter}" | ||
| for wyk_letter, occurrences in itertools.groupby( | ||
| label_group, key=lambda x: x[2] | ||
| ) | ||
| ) | ||
|
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| element_wyckoffs += [wyckoff_counts_str] | ||
|
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| all_wyckoffs = canonicalize_wyckoffs("_".join(element_wyckoffs), spg_num) | ||
|
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| # Build prototype label | ||
| prototype_label = ( | ||
| f"{get_prototype_formula(struct.composition)}_" | ||
| f"{get_pearson_symbol(symmetry_data)}_" | ||
| f"{spg_num}_{all_wyckoffs}:{struct.chemical_system}" | ||
| ) | ||
|
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| # Verify multiplicities match composition | ||
| observed_formula = Composition(element_dict).reduced_formula | ||
| expected_formula = struct.composition.reduced_formula | ||
| if observed_formula != expected_formula: | ||
| err_msg = ( | ||
| f"Invalid WP multiplicities - {prototype_label}, expected " | ||
| f"{observed_formula} to be {expected_formula}" | ||
| ) | ||
| if raise_errors: | ||
| raise ValueError(err_msg) | ||
| return err_msg | ||
|
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||
| return prototype_label |
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