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
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
|
# Copyright (c) 2024, 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.
"""Unit tests for the CJSON writer."""
import json
import os
from math import sqrt
import cclib
__filedir__ = os.path.dirname(__file__)
__filepath__ = os.path.realpath(__filedir__)
__datadir__ = os.path.join(__filepath__, "..", "..")
class CJSONWriterTest:
"""Unit tests for the CJSON writer."""
def test_init(self):
"""Does the class initialize correctly?"""
fpath = os.path.join(__datadir__, "data/ADF/basicADF2007.01/dvb_gopt.adfout")
data = cclib.io.ccread(fpath)
cjson = cclib.io.cjsonwriter.CJSON(data)
# The object should keep the ccData instance passed to its constructor.
assert cjson.ccdata == data
def test_cjson_generation(self):
"""Does the CJSON format get generated properly?"""
fpath = os.path.join(__datadir__, "data/ADF/basicADF2007.01/NH3.adfout")
data = cclib.io.ccread(fpath)
cjson = cclib.io.cjsonwriter.CJSON(data).generate_repr()
# The data available in the cjson and ccdata objects should be equal.
json_data = json.loads(cjson)
number_of_atoms = json_data["properties"]["number of atoms"]
assert number_of_atoms == data.natom
dipole_moment = json_data["properties"]["total dipole moment"]
assert round(abs(dipole_moment - sqrt(sum(data.moments[1] ** 2))), 7) == 0
# Ensure the bond connectivity index starts from 0
bonds = json_data.get("bonds", None)
assert bonds is not None
indices = bonds["connections"]["index"]
assert min(indices) == 0
assert max(indices) < number_of_atoms
def test_zero_dipole_moment(self):
"""Does the CJSON writer handle zero dipole moment correctly?"""
fpath = os.path.join(__datadir__, "data/GAMESS/basicGAMESS-US2017/C_bigbasis.out")
data = cclib.io.ccopen(fpath).parse()
cjson = cclib.io.cjsonwriter.CJSON(data).generate_repr()
json_data = json.loads(cjson)
assert round(abs(json_data["properties"]["total dipole moment"]), 7) == 0
def test_missing_dipole_moment(self):
"""Does the CJSON writer handle missing properties correctly?"""
fpath = os.path.join(__datadir__, "data/GAMESS/basicGAMESS-US2017/C_bigbasis.out")
data = cclib.io.ccopen(fpath).parse()
del data.moments
cjson = cclib.io.cjsonwriter.CJSON(data).generate_repr()
json_data = json.loads(cjson)
assert "total dipole moment" not in json_data["properties"]
|
