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
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
|
import numpy as np
import pytest
from monty.serialization import loadfn
from pymatgen.analysis.structure_matcher import StructureMatcher
from pymatgen.entries.computed_entries import ComputedEntry
try:
from emmet.core.mobility.migrationgraph import MigrationGraphDoc
except (ModuleNotFoundError,ImportError):
pytest.skip(reason="Install pymatgen-analysis-diffusion to use MigrationGraphDoc",
allow_module_level=True)
@pytest.fixture(scope="session")
def get_entries(test_dir):
entry_Li = ComputedEntry("Li", -1.90753119)
entries = loadfn(test_dir / "mobility/LiMnP2O7_batt.json")
return (entries, entry_Li)
@pytest.fixture(scope="session")
def migration_graph_prop():
"""
set the expected parameters for the migrationgraph
"""
expected_properties = {
"LiMnP2O7": {
"max_distance": 5,
"num_uhops": 8,
"longest_hop": 4.92647,
"shortest_hop": 2.77240,
"min_length_sc": 7,
"minmax_num_atoms": (80, 160),
}
}
return expected_properties
@pytest.fixture(scope="session")
def mg_for_sc_fields(test_dir):
"""
get MigrationGraph object generated with methods from pymatgen.analysis.diffusion for testing generate_sc_fields
"""
mg_for_sc = loadfn(test_dir / "mobility/mg_for_sc.json")
return mg_for_sc
@pytest.mark.skip(
reason="Incompatible with Pymatgen>=2024.9.10, regression testing in progress..."
)
def test_from_entries_and_distance(migration_graph_prop, get_entries):
for expected in migration_graph_prop.values():
mgdoc = MigrationGraphDoc.from_entries_and_distance(
battery_id="mp-1234",
grouped_entries=get_entries[0],
working_ion_entry=get_entries[1],
hop_cutoff=5,
populate_sc_fields=True,
min_length_sc=7,
minmax_num_atoms=(80, 160),
)
mg = mgdoc.migration_graph
res_d = {
"max_distance": mgdoc.hop_cutoff,
"num_uhops": len(mg.unique_hops),
"longest_hop": sorted(
mg.unique_hops.items(), key=lambda x: x[1]["hop_distance"]
)[-1][1]["hop_distance"],
"shortest_hop": sorted(
mg.unique_hops.items(), key=lambda x: x[1]["hop_distance"]
)[0][1]["hop_distance"],
"min_length_sc": mgdoc.min_length_sc,
"minmax_num_atoms": mgdoc.minmax_num_atoms,
}
for k, v in expected.items():
assert res_d[k] == pytest.approx(v, 0.01)
def test_generate_sc_fields(mg_for_sc_fields):
sm = StructureMatcher()
(
host_sc,
sc_mat,
min_length,
min_max_num_atoms,
coords_dict,
combo,
) = MigrationGraphDoc.generate_sc_fields(mg_for_sc_fields, 7, (80, 160), sm)
sc_mat_inv = np.linalg.inv(sc_mat)
expected_sc_list = []
for one_hop in mg_for_sc_fields.unique_hops.values():
host_sc_insert = host_sc.copy()
host_sc_insert.insert(0, "Li", np.dot(one_hop["ipos"], sc_mat_inv))
host_sc_insert.insert(0, "Li", np.dot(one_hop["epos"], sc_mat_inv))
expected_sc_list.append(host_sc_insert)
for one_combo in combo:
hop_sc = host_sc.copy()
sc_iindex, sc_eindex = list(map(int, one_combo.split("+")))
sc_isite = coords_dict[sc_iindex]["site_frac_coords"]
sc_esite = coords_dict[sc_eindex]["site_frac_coords"]
hop_sc.insert(0, "Li", sc_isite)
hop_sc.insert(0, "Li", sc_esite)
check_sc_list = [sm.fit(hop_sc, check_sc) for check_sc in expected_sc_list]
assert sum(check_sc_list) >= 1
@pytest.mark.skip(
reason="Incompatible with Pymatgen>=2024.9.10, regression testing in progress..."
)
def test_get_distinct_hop_sites(get_entries):
mgdoc = MigrationGraphDoc.from_entries_and_distance(
battery_id="mp-1234",
grouped_entries=get_entries[0],
working_ion_entry=get_entries[1],
hop_cutoff=5,
populate_sc_fields=True,
min_length_sc=7,
minmax_num_atoms=(80, 160),
)
(
dis_sites_list,
dis_combo_list,
combo_mapping,
) = MigrationGraphDoc.get_distinct_hop_sites(
mgdoc.inserted_ion_coords, mgdoc.insert_coords_combo
)
for one_test_combo in ["0+1", "0+2", "0+3", "0+4", "0+5", "0+6", "1+7", "1+2"]:
assert one_test_combo in dis_combo_list
assert combo_mapping == {
"0+1": "9+4",
"0+2": "9+8",
"0+3": "9+6",
"0+4": "9+16",
"0+5": "9+17",
"0+6": "9+13",
"1+7": "4+0",
"1+2": "4+8",
}
|
