"""Module to check interatomic distances."""
# Standard library imports
import itertools
from typing import Union, List, Tuple
# Internal library imports
from aim2dat.strct import Structure
from aim2dat.utils.element_properties import get_atomic_radius
[docs]
class DistanceThresholdError(ValueError):
"""Error in case distances between atom sites are too short or too long."""
pass
def _build_distance_dict(
dist_threshold: Union[list, dict, tuple, str, float, int], structure, guest_structure=None
) -> Tuple[Union[dict, None], float]:
"""Construct dictionary from disth_threshold parameter."""
elements = set(structure._element_dict.keys())
if guest_structure is not None:
elements = elements.union(guest_structure._element_dict.keys())
el_pairs = itertools.combinations_with_replacement(elements, 2)
if dist_threshold is None:
return None, 0.0
# If dist_threshold is dict, make sure that it contains index or element pairs and check that
# value is list:
elif isinstance(dist_threshold, dict):
new_dict = {}
for key, val in dist_threshold.items():
if len(key) != 2:
raise ValueError(
"`dist_threshold` needs to have keys with length 2 containing site "
+ "indices or element symbols."
)
if not (all(isinstance(k, int) for k in key) or all(isinstance(k, str) for k in key)):
raise ValueError(
"`dist_threshold` needs to have keys of type List[str/int] containing "
+ "site indices or element symbols."
)
if isinstance(val, (float, int)):
val = [val, None]
new_dict[tuple(sorted(key))] = val
dist_threshold = new_dict
# Transfer string to element-pair dict:
elif isinstance(dist_threshold, str):
tol = 1.0
if "+" in dist_threshold:
dist_threshold, tol = dist_threshold.split("+")
tol = 1.0 + float(tol) / 100.0
elif "-" in dist_threshold:
dist_threshold, tol = dist_threshold.split("-")
tol = 1.0 - float(tol) / 100.0
atomic_radii = {el: get_atomic_radius(el, radius_type=dist_threshold) for el in elements}
dist_threshold = {
tuple(sorted(pair)): [(atomic_radii[pair[0]] + atomic_radii[pair[1]]) * tol, None]
for pair in el_pairs
}
# Transfer list of min/max values to element-pair dict:
elif isinstance(dist_threshold, (list, tuple)):
dist_threshold = {tuple(sorted(pair)): dist_threshold for pair in el_pairs}
# Transfer float/int to element-pair dict:
elif isinstance(dist_threshold, (float, int)):
dist_threshold = {tuple(sorted(pair)): [dist_threshold, None] for pair in el_pairs}
else:
raise TypeError("`dist_threshold` needs to be of type int/float/list/tuple/dict or None.")
return dist_threshold, min(val[0] for val in dist_threshold.values())
def _check_distances(
structure: Structure,
indices: List[int],
dist_threshold: Union[dict, list, float, int, None],
distance_dict: Union[dict, None],
silent: bool,
) -> bool:
"""
Check if the distance between the specified atoms and all other atoms in the structure
is in the given threshold.
Parameters
----------
structure : aim2dat.strct.Structure
The structure containing the atom positions.
indices : list of int
A list of indices identifying the atoms in the structure whose distances are to be
checked.
dist_threshold : dict, list, float, int, str or None (optional)
Check the distances between all site pairs to ensure that none of the changed atoms
collide or are too far apart. For example, ``0.8`` to ensure a minimum distance of
``0.8`` for all site pairs. A list ``[0.8, 1.5]`` adds a check for the maximum distance
as well. Giving a dictionary ``{("C", "H"): 0.8, (0, 4): 0.8}`` allows distance checks
for individual pairs of elements or site indices. Specifying an atomic radius type as
str, e.g. ``covalent+10`` sets the minimum threshold to the sum of covalent radii plus
10%.
distance_dict : dict
Dictionary containing element or index tuples as keys and distance thresholds as values.
silent : bool (optional)
If True, no error is raised when atoms are too close. If False, a ValueError is raised
when atoms are too close to each other.
Returns
----------
bool
True if all distances are in between the threshold, or no check was performed.
False if any distance outside the threshold and `silent` is False.
Raises
----------
ValueError
If any distance between atoms is outside the threshold and `silent` is False.
"""
if dist_threshold is not None:
distance_dict, _ = _build_distance_dict(dist_threshold, structure)
if distance_dict is None:
return True
# Calculate pair-wise distances:
other_indices = [i for i in range(len(structure)) if i not in indices]
dists = structure.calculate_distance(other_indices, indices, backfold_positions=True)
for idx_pair, dist in dists.items():
threshold = distance_dict.get(tuple(sorted(idx_pair)), None)
if threshold is None:
el_pair = tuple(
sorted([structure.elements[idx_pair[0]], structure.elements[idx_pair[1]]])
)
threshold = distance_dict.get(el_pair, None)
if threshold is None:
continue
if dist < threshold[0]:
if silent:
return False
raise DistanceThresholdError(
f"Atoms {idx_pair[0]} and {idx_pair[1]} are too close to each other."
)
if threshold[1] is not None and dist > threshold[1]:
if silent:
return False
raise DistanceThresholdError(
f"Atoms {idx_pair[0]} and {idx_pair[1]} are too far from each other."
)
return True