Skip to content

Commit fa030cb

Browse files
alongdalongd
committed
Tests: Linear TS Job Adapter
1 parent 92e8061 commit fa030cb

1 file changed

Lines changed: 179 additions & 0 deletions

File tree

‎arc/job/adapters/ts/linear_test.py‎

Lines changed: 179 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,179 @@
1+
#!/usr/bin/env python3
2+
# encoding: utf-8
3+
4+
"""
5+
This module contains unit tests of the arc.job.adapters.ts.heuristics module
6+
"""
7+
8+
import unittest
9+
import shutil
10+
11+
from arc.common import ARC_PATH, _check_r_n_p_symbols_between_rmg_and_arc_rxns, almost_equal_coords
12+
from arc.job.adapters.ts.linear import (LinearAdapter,
13+
average_zmat_params,
14+
get_rxn_weight,
15+
get_weight,
16+
interpolate_isomerization,
17+
)
18+
from arc.reaction import ARCReaction
19+
from arc.rmgdb import load_families_only, make_rmg_database_object
20+
from arc.species.converter import str_to_xyz, zmat_to_xyz, xyz_to_str
21+
from arc.species.species import ARCSpecies
22+
from arc.species.zmat import _compare_zmats
23+
24+
25+
class TestHeuristicsAdapter(unittest.TestCase):
26+
"""
27+
Contains unit tests for the HeuristicsAdapter class.
28+
"""
29+
30+
@classmethod
31+
def setUpClass(cls):
32+
"""
33+
A method that is run before all unit tests in this class.
34+
"""
35+
cls.maxDiff = None
36+
# cls.rmgdb = make_rmg_database_object()
37+
# load_families_only(cls.rmgdb)
38+
39+
def test_average_zmat_params(self):
40+
"""Test the average_zmat_params() function."""
41+
zmat_1 = {'symbols': ('H', 'H'),
42+
'coords': ((None, None, None),
43+
('R_1_0', None, None)),
44+
'vars': {'R_1_0': 0.7},
45+
'map': {0: 0, 1: 1}}
46+
zmat_2 = {'symbols': ('H', 'H'),
47+
'coords': ((None, None, None),
48+
('R_1_0', None, None)),
49+
'vars': {'R_1_0': 1.3},
50+
'map': {0: 0, 1: 1}}
51+
expected_zmat = {'symbols': ('H', 'H'),
52+
'coords': ((None, None, None),
53+
('R_1_0', None, None)),
54+
'vars': {'R_1_0': 1.0},
55+
'map': {0: 0, 1: 1}}
56+
zmat = average_zmat_params(zmat_1, zmat_2)
57+
self.assertTrue(_compare_zmats(zmat, expected_zmat))
58+
59+
expected_zmat = {'symbols': ('H', 'H'),
60+
'coords': ((None, None, None),
61+
('R_1_0', None, None)),
62+
'vars': {'R_1_0': 0.85},
63+
'map': {0: 0, 1: 1}}
64+
zmat = average_zmat_params(zmat_1, zmat_2, weight=0.25)
65+
self.assertTrue(_compare_zmats(zmat, expected_zmat))
66+
zmat = average_zmat_params(zmat_2, zmat_1, weight=0.75)
67+
self.assertTrue(_compare_zmats(zmat, expected_zmat))
68+
69+
zmat_1 = {'symbols': ('C', 'N', 'H', 'H', 'H', 'H', 'H'),
70+
'coords': ((None, None, None), ('R_1_0', None, None), ('R_2|4_0|0', 'A_2|4_0|0_1|1', None),
71+
('R_3|6_1|1', 'A_3|6_1|1_0|0', 'D_3_1_0_2'),
72+
('R_2|4_0|0', 'A_2|4_0|0_1|1', 'D_4_0_1_3'), ('R_5_0', 'A_5_0_1', 'D_5_0_1_4'),
73+
('R_3|6_1|1', 'A_3|6_1|1_0|0', 'D_6_1_0_5')),
74+
'vars': {'R_1_0': 1.451965854148702, 'D_3_1_0_2': 60.83821034525936,
75+
'D_4_0_1_3': 301.30263742432356, 'R_5_0': 1.0936965384360282,
76+
'A_5_0_1': 110.59878027260544, 'D_5_0_1_4': 239.76779188408136,
77+
'D_6_1_0_5': 65.17113681053117, 'R_2|4_0|0': 1.0935188594180785,
78+
'R_3|6_1|1': 1.019169330302324, 'A_2|4_0|0_1|1': 110.20495980110817,
79+
'A_3|6_1|1_0|0': 109.41187648524644},
80+
'map': {0: 0, 1: 1, 2: 2, 3: 5, 4: 3, 5: 4, 6: 6}}
81+
zmat_2 = {'symbols': ('C', 'N', 'H', 'H', 'H', 'H', 'H'),
82+
'coords': ((None, None, None), ('R_1_0', None, None), ('R_2|4_0|0', 'A_2|4_0|0_1|1', None),
83+
('R_3|6_1|1', 'A_3|6_1|1_0|0', 'D_3_1_0_2'),
84+
('R_2|4_0|0', 'A_2|4_0|0_1|1', 'D_4_0_1_3'), ('R_5_0', 'A_5_0_1', 'D_5_0_1_4'),
85+
('R_3|6_1|1', 'A_3|6_1|1_0|0', 'D_6_1_0_5')),
86+
'vars': {'R_1_0': 1.2, 'D_3_1_0_2': 50,
87+
'D_4_0_1_3': 250, 'R_5_0': 1.0936965384360282,
88+
'A_5_0_1': 110.59878027260544, 'D_5_0_1_4': 239.76779188408136,
89+
'D_6_1_0_5': 120, 'R_2|4_0|0': 1.0935188594180785,
90+
'R_3|6_1|1': 1.6, 'A_2|4_0|0_1|1': 110.20495980110817,
91+
'A_3|6_1|1_0|0': 109.41187648524644},
92+
'map': {0: 0, 1: 1, 2: 2, 3: 5, 4: 3, 5: 4, 6: 6}}
93+
expected_zmat = {'symbols': ('C', 'N', 'H', 'H', 'H', 'H', 'H'),
94+
'coords': ((None, None, None), ('R_1_0', None, None), ('R_2|4_0|0', 'A_2|4_0|0_1|1', None),
95+
('R_3|6_1|1', 'A_3|6_1|1_0|0', 'D_3_1_0_2'), ('R_2|4_0|0', 'A_2|4_0|0_1|1', 'D_4_0_1_3'),
96+
('R_5_0', 'A_5_0_1', 'D_5_0_1_4'), ('R_3|6_1|1', 'A_3|6_1|1_0|0', 'D_6_1_0_5')),
97+
'vars': {'R_1_0': 1.3259829270743508, 'D_3_1_0_2': 55.419105172629685,
98+
'D_4_0_1_3': 275.6513187121618, 'R_5_0': 1.0936965384360282,
99+
'A_5_0_1': 110.59878027260544, 'D_5_0_1_4': 239.76779188408136,
100+
'D_6_1_0_5': 92.58556840526558, 'R_2|4_0|0': 1.0935188594180785,
101+
'R_3|6_1|1': 1.309584665151162, 'A_2|4_0|0_1|1': 110.20495980110817,
102+
'A_3|6_1|1_0|0': 109.41187648524644},
103+
'map': {0: 0, 1: 1, 2: 2, 3: 5, 4: 3, 5: 4, 6: 6}}
104+
zmat = average_zmat_params(zmat_1, zmat_2)
105+
self.assertTrue(_compare_zmats(zmat, expected_zmat))
106+
107+
def test_get_weight(self):
108+
"""Test the get_weight() function."""
109+
self.assertEqual(get_weight([0], [0], 4), 0.5) # 4 / 8
110+
self.assertEqual(get_weight([0], [8], 12), 0.75) # 12 / 20
111+
self.assertEqual(get_weight([0], [2], 6), 0.6) # 6 / 10
112+
self.assertEqual(get_weight([10], [0], 30), 0.4) # 20 / 50
113+
self.assertEqual(get_weight([20], [10], 40), 0.4) # 20 / 50
114+
self.assertIsNone(get_weight([20], [None], 40), 0.4) # 20 / 50
115+
self.assertEqual(get_weight([8, 2], [0], 30), 0.4) # 20 / 50
116+
self.assertEqual(get_weight([4, 1], [5.5, 1.5], 11), 0.6) # 6 / 10
117+
118+
def test_get_rxn_weight(self):
119+
"""Test the get_rxn_weight() function."""
120+
rxn_1 = ARCReaction(r_species=[ARCSpecies(label='HO2', smiles='[O]O'),
121+
ARCSpecies(label='NH', smiles='[NH]')],
122+
p_species=[ARCSpecies(label='N', smiles='[N]'),
123+
ARCSpecies(label='H2O2', smiles='OO')])
124+
rxn_1.r_species[0].e0 = 252.0
125+
rxn_1.r_species[1].e0 = 100.5
126+
rxn_1.p_species[0].e0 = 116.0
127+
rxn_1.p_species[1].e0 = 200.3
128+
rxn_1.ts_species = ARCSpecies(label='TS', is_ts=True)
129+
rxn_1.ts_species.e0 = 391.6
130+
self.assertAlmostEquals(get_rxn_weight(rxn_1), 0.3417832)
131+
132+
def test_interpolate_isomerization(self):
133+
"""Test the interpolate_isomerization() function."""
134+
nc3h7_xyz = """C 0.00375165 -0.48895802 -1.20586379
135+
C 0.00375165 -0.48895802 0.28487510
136+
C 0.00375165 0.91997987 0.85403684
137+
H 0.41748586 -1.33492098 -1.74315104
138+
H -0.57506729 0.24145491 -1.76006154
139+
H -0.87717095 -1.03203740 0.64280162
140+
H 0.88948616 -1.02465371 0.64296621
141+
H 0.88512433 1.48038223 0.52412379
142+
H 0.01450405 0.88584135 1.94817394
143+
H -0.88837301 1.47376959 0.54233121"""
144+
ic3h7_xyz = """C -0.40735690 -0.74240205 -0.34312948
145+
C 0.38155377 -0.25604705 0.82450968
146+
C 0.54634593 1.25448345 0.81064511
147+
H 0.00637731 -1.58836501 -0.88041673
148+
H -0.98617584 -0.01198912 -0.89732723
149+
H -1.29710684 -1.29092340 0.08598983
150+
H 1.36955428 -0.72869684 0.81102246
151+
H 1.06044877 1.58846788 -0.09702437
152+
H 1.13774084 1.57830484 1.67308862
153+
H -0.42424546 1.75989927 0.85794283"""
154+
rxn = ARCReaction(r_species=[ARCSpecies(label='nC3H7', smiles='[CH2]CC', xyz=nc3h7_xyz)],
155+
p_species=[ARCSpecies(label='iC3H7', smiles='C[CH]C', xyz=ic3h7_xyz)])
156+
expected_ts_xyz = str_to_xyz("""C 0.01099731 -0.46789926 -1.15958911
157+
C 0.01099731 -0.46789926 0.33114978
158+
C 0.01099731 0.94103865 0.90031155
159+
H 0.57795661 -1.24174248 -1.65467180
160+
H -0.39690222 0.34527841 -1.69240298
161+
H -1.19440431 -1.28933062 -0.47327539
162+
H 0.89689057 -1.16420498 0.45967951
163+
H 0.76979130 1.33747945 0.33815513
164+
H -0.04544494 0.70455273 1.77835334
165+
H -1.00071642 1.24557408 0.38839197""")
166+
ts_xyz = interpolate_isomerization(rxn, use_weights=False)
167+
self.assertTrue(almost_equal_coords(ts_xyz, expected_ts_xyz))
168+
169+
@classmethod
170+
def tearDownClass(cls):
171+
"""
172+
A function that is run ONCE after all unit tests in this class.
173+
Delete all project directories created during these unit tests.
174+
"""
175+
pass
176+
177+
178+
if __name__ == '__main__':
179+
unittest.main(testRunner=unittest.TextTestRunner(verbosity=2))

0 commit comments

Comments
 (0)