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
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
|
""" Core definition of a Materials Document """
from __future__ import annotations
from datetime import datetime
from typing import List, Mapping, Type, TypeVar, Union, Optional
from pydantic import BaseModel, Field, field_validator
from pymatgen.core import Structure
from pymatgen.core.structure import Molecule
from emmet.core.mpid import MPID, MPculeID
from emmet.core.structure import MoleculeMetadata, StructureMetadata
from emmet.core.vasp.validation import DeprecationMessage
from emmet.core.common import convert_datetime
class PropertyOrigin(BaseModel):
"""
Provenance document for the origin of properties in a material document
"""
name: str = Field(..., description="The property name")
task_id: Union[MPID, MPculeID] = Field(
..., description="The calculation ID this property comes from"
)
last_updated: datetime = Field( # type: ignore
description="The timestamp when this calculation was last updated",
default_factory=datetime.utcnow,
)
@field_validator("last_updated", mode="before")
@classmethod
def handle_datetime(cls, v):
return convert_datetime(cls, v)
T = TypeVar("T", bound="MaterialsDoc")
S = TypeVar("S", bound="CoreMoleculeDoc")
class MaterialsDoc(StructureMetadata):
"""
Definition for a core Materials Document
"""
# Only material_id is required for all documents
material_id: MPID = Field(
...,
description="The Materials Project ID of the material, used as a universal reference across property documents."
"This comes in the form: mp-******.",
)
structure: Structure = Field(
...,
description="The structure of the this material.",
)
deprecated: bool = Field(
True,
description="Whether this materials document is deprecated.",
)
deprecation_reasons: Optional[List[Union[DeprecationMessage, str]]] = Field(
None,
description="List of deprecation tags detailing why this materials document isn't valid.",
)
initial_structures: List[Structure] = Field(
[],
description="Initial structures used in the DFT optimizations corresponding to this material.",
)
task_ids: List[MPID] = Field(
[],
description="List of Calculations IDs used to make this Materials Document.",
)
deprecated_tasks: List[str] = Field([], title="Deprecated Tasks")
calc_types: Optional[Mapping[str, str]] = Field(
None,
description="Calculation types for all the calculations that make up this material.",
)
last_updated: datetime = Field(
description="Timestamp for when this document was last updated.",
default_factory=datetime.utcnow,
)
created_at: datetime = Field(
description="Timestamp for when this material document was first created.",
default_factory=datetime.utcnow,
)
origins: Optional[List[PropertyOrigin]] = Field(
None, description="Dictionary for tracking the provenance of properties."
)
warnings: List[str] = Field(
[], description="Any warnings related to this material."
)
@classmethod
def from_structure(
cls: Type[T], structure: Structure, material_id: MPID, **kwargs
) -> T: # type: ignore[override]
"""
Builds a materials document using the minimal amount of information
"""
return super().from_structure( # type: ignore
meta_structure=structure,
material_id=material_id,
structure=structure,
**kwargs,
)
class CoreMoleculeDoc(MoleculeMetadata):
"""
Definition for a core Molecule Document
"""
# Only molecule_id is required for all documents
molecule_id: MPculeID = Field(
...,
description="The ID of this molecule, used as a universal reference across property documents."
"This comes in the form of an MPID (or int) or MPculeID (or str)",
)
molecule: Molecule = Field(
...,
description="The best (typically meaning lowest in energy) structure for this molecule",
)
deprecated: bool = Field(
True,
description="Whether this molecule document is deprecated.",
)
# TODO: Why might a molecule be deprecated?
deprecation_reasons: Optional[List[str]] = Field(
None,
description="List of deprecation tags detailing why this molecules document isn't valid",
)
initial_molecules: List[Molecule] = Field(
[],
description="Initial molecules used in the DFT geometry optimizations corresponding to this molecule",
)
task_ids: List[MPID] = Field(
[],
title="Calculation IDs",
description="List of Calculations IDs used to make this Molecule Document",
)
# TODO: Should this be MPID?
deprecated_tasks: List[str] = Field([], title="Deprecated Tasks")
calc_types: Optional[Mapping[str, str]] = Field(
None,
description="Calculation types for all the tasks that make up this molecule",
)
last_updated: datetime = Field(
description="Timestamp for when this document was last updated",
default_factory=datetime.utcnow,
)
created_at: datetime = Field(
description="Timestamp for when this document was first created",
default_factory=datetime.utcnow,
)
origins: Optional[List[PropertyOrigin]] = Field(
None, description="Dictionary for tracking the provenance of properties"
)
warnings: List[str] = Field([], description="Any warnings related to this molecule")
@classmethod
def from_molecule(
cls: Type[S], molecule: Molecule, molecule_id: MPculeID, **kwargs
) -> S: # type: ignore[override]
"""
Builds a molecule document using the minimal amount of information
"""
return super().from_molecule( # type: ignore
meta_molecule=molecule, molecule_id=molecule_id, molecule=molecule, **kwargs
)
|
