# MIT License
#
# Copyright (c) 2024-2025 Inverse Materials Design Group
#
# Author: Ihor Radchenko <yantar92@posteo.net>
#
# This file is a part of IMDgroup-pymatgen package
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
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"""This module implements helper functions to work with ATAT."""
import numpy as np
from pymatgen.core import DummySpecies, Structure
from IMDgroup.pymatgen.core.structure import\
structure_strain, structure_distance, get_matched_structure
[docs]
def check_volume_distortion(
str_before: Structure,
str_after: Structure,
# 0.1 is what is done by ATAT in checkcell subroutine
threshold: float = 0.1) -> bool:
"""Check whether lattice distortion between two structures is acceptable.
The distortion is the norm of the engineering strain tensor.
A distortion below ``threshold`` is considered acceptable.
The default threshold follows ATAT's ``checkcell`` subroutine.
Args:
str_before: Initial structure.
str_after: Deformed structure.
threshold: Max allowed distortion (default: 0.1).
Returns:
bool: True if distortion is below threshold, False otherwise.
"""
strain = structure_strain(str_before, str_after)
distortion = np.linalg.norm(strain)
if distortion < threshold:
return True
return False
[docs]
def check_sublattice_flip(
str_before: Structure,
str_after: Structure,
sublattice: Structure) -> bool:
"""Check whether the relaxed sublattice configuration is preserved.
Returns True when ``str_after`` occupies the same sublattice
configuration as ``str_before``, when compared against the
reference ``sublattice``.
The species scanned by cluster expansion must be marked with the
same dummy species name (e.g. X) in all arguments. For example,
in an ATAT Li,Vac system, both Li and Vac should be replaced with
X.
Args:
str_before: Structure before relaxation.
str_after: Structure after relaxation.
sublattice: Full sublattice with all sites occupied (as in str.in).
Returns:
bool: True if the sublattice configuration is preserved.
"""
# First, scale STR_AFTER lattice to fit STR_BEFORE and SUBLATTICE
# Assume that STR_BEFORE and SUBLATTICE have the same lattices
str_after_normalized = str_after.copy()
str_after_normalized.lattice = str_before.lattice
dist_relax = structure_distance(str_before, str_after_normalized)
# Replace all species with X to compare with anonymous sublattice
dist_sublattice = structure_distance(
str_after_normalized, sublattice,
# Compare specie-insensitively
match_first=True,
match_species=False)
if np.isclose(dist_relax, dist_sublattice, rtol=0.001):
return True
return False
[docs]
def fit_sublattice_to_structure(
sublattice: Structure, structure: Structure) -> Structure:
"""Adjust a reference sublattice to match a relaxed structure.
Useful for building a new ``str.out`` when the structure has
flipped away from the initial sublattice guess (see
:func:`check_sublattice_flip`). Use ``'X'`` dummy species in place
of vacancies.
Args:
sublattice: Reference sublattice (as from str.in).
structure: Relaxed structure with possible sublattice flip.
Returns:
Structure: Adjusted sublattice matching the relaxed structure.
"""
structure = structure.copy()
# Force the lattice to match. Needed for get_matched_structure.
structure.lattice = sublattice.lattice
sublattice2 = get_matched_structure(
structure, sublattice, match_species=False)
for idx, site in enumerate(sublattice2):
if idx < len(structure):
site.species = structure[idx].species
else:
site.species = DummySpecies('X')
# keep the original site order
sublattice2 = get_matched_structure(sublattice, sublattice2, match_species=False)
return sublattice2