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
|
import logging
from typing import Dict, List, Any
import numpy as np
from pydantic import Field
from pymatgen.analysis.graphs import StructureGraph
from pymatgen.analysis.local_env import NearNeighbors
from emmet.core.material_property import PropertyDoc
AVAILABLE_METHODS = {nn.__name__: nn for nn in NearNeighbors.__subclasses__()}
class BondingDoc(PropertyDoc):
"""Structure graphs representing chemical bonds calculated from structure
using near neighbor strategies as defined in pymatgen."""
property_name: str = "bonding"
structure_graph: StructureGraph = Field(
description="Structure graph",
)
method: str = Field(description="Method used to compute structure graph.")
bond_types: Dict[str, List[float]] = Field(
description="Dictionary of bond types to their length, e.g. a Fe-O to "
"a list of the lengths of Fe-O bonds in Angstrom."
)
bond_length_stats: Dict[str, Any] = Field(
description="Dictionary of statistics of bonds in structure "
"with keys all_weights, min, max, mean and variance."
)
coordination_envs: List[str] = Field(
description="List of co-ordination environments, e.g. ['Mo-S(6)', 'S-Mo(3)']."
)
coordination_envs_anonymous: List[str] = Field(
description="List of co-ordination environments without elements "
"present, e.g. ['A-B(6)', 'A-B(3)']."
)
@classmethod
def from_structure(
cls,
structure,
material_id,
preferred_methods=(
"CrystalNN",
"MinimumDistanceNN",
),
**kwargs
):
"""
Calculate
:param structure: ideally an oxidation state-decorated structure
:param material_id: mpid
:param preferred_methods: list of strings of NearNeighbor classes or NearNeighbor instances
:param deprecated: whether source material is or is not deprecated
:param kwargs: to pass to PropertyDoc
:return:
"""
bonding_info = None
preferred_methods = [ # type: ignore
AVAILABLE_METHODS[method]() if isinstance(method, str) else method
for method in preferred_methods
]
for method in preferred_methods:
try:
sg = StructureGraph.with_local_env_strategy(structure, method)
# ensure edge weights are specifically bond lengths
edge_weights = []
for u, v, d in sg.graph.edges(data=True):
jimage = np.array(d["to_jimage"])
dist = sg.structure.get_distance(u, v, jimage=jimage)
edge_weights.append((u, v, d["to_jimage"], dist))
for u, v, to_jimage, dist in edge_weights:
sg.alter_edge(u, v, to_jimage=to_jimage, new_weight=dist)
bonding_info = {
"method": method.__class__.__name__,
"structure_graph": sg,
"bond_types": sg.types_and_weights_of_connections,
"bond_length_stats": sg.weight_statistics,
"coordination_envs": sg.types_of_coordination_environments(),
"coordination_envs_anonymous": sg.types_of_coordination_environments(
anonymous=True
),
}
break
except Exception as e:
logging.warning(
"Failed to calculate bonding: {} {} {}".format(
material_id, method, e
)
)
if bonding_info:
return super().from_structure(
meta_structure=structure,
material_id=material_id,
**bonding_info,
**kwargs
)
|
