Source code for mbgdml.models.gap_model

# MIT License
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# Copyright (c) 2022-2023, Alex M. Maldonado
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import hashlib
import numpy as np
from .base import Model
from ..logger import GDMLLogger

try:
    import quippy

    _HAS_QUIPPY = True
except ImportError:
    _HAS_QUIPPY = False

log = GDMLLogger(__name__)

# pylint: disable-next=invalid-name
class gapModel(Model):
    def __init__(
        self,
        model_path,
        comp_ids,
        criteria=None,
    ):
        """
        Parameters
        ----------
        model_path : :obj:`str`
            Path to GAP xml file.
        comp_ids : ``iterable``
            Model component IDs that relate entity IDs of a structure to a
            fragment label.
        criteria : :obj:`mbgdml.descriptors.Criteria`, default: :obj:`None`
            Initialized descriptor criteria for accepting a structure based on
            a descriptor and cutoff.
        """
        assert _HAS_QUIPPY

        super().__init__(criteria)
        self.type = "gap"
        self.gap = quippy.potential.Potential(param_filename=model_path)
        if isinstance(comp_ids, (list, tuple)):
            comp_ids = np.array(comp_ids)
        self.comp_ids = comp_ids
        self.nbody_order = len(comp_ids)

        # GAP MD5
        with open(model_path, "r", encoding="utf-8") as f:
            gap_lines = f.readlines()

        md5_hash = hashlib.md5()
        for gap_line in gap_lines:
            md5_hash.update(hashlib.md5(repr(gap_line).encode()).digest())
        self.md5 = md5_hash.hexdigest()