1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
|
# -*- coding: utf-8 -*-
#
# Copyright (c) 2023, the cclib development team
#
# This file is part of cclib (http://cclib.github.io) and is distributed under
# the terms of the BSD 3-Clause License.
"""Functions used across multiple data tests."""
import itertools
import numpy
from cclib.parser.data import ccData
def get_minimum_carbon_separation(data: ccData) -> float:
"""Returns minimum carbon distance for any coordinates.
Note that atomcoords is 3D, and we will take the minimum
over all coordinates and combinations of carbon atoms.
"""
icarbons = numpy.arange(data.natom)[data.atomnos == 6]
mindist = 999
for i, j in itertools.combinations(icarbons, 2):
vectors = data.atomcoords[:, i] - data.atomcoords[:, j]
distances = numpy.linalg.norm(vectors, axis=1)
mindist = min(mindist, min(distances))
return mindist
|
