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
|
from __future__ import annotations
from pydantic import Field
from emmet.core.tasks import TaskDoc, _VOLUMETRIC_FILES
from typing import TYPE_CHECKING, Optional
from pymatgen.analysis.defects.core import Defect
from monty.json import MontyDecoder
from pydantic import BaseModel
if TYPE_CHECKING:
from typing import Any, Dict, Tuple, Union
from pathlib import Path
mdecoder = MontyDecoder().process_decoded
class DefectInfo(BaseModel):
"""Information related to a point defect."""
defect_name: str = Field(
title="The name of the defect",
)
bulk_formula: str = Field(
title="Bulk Formula",
description="Formula of the bulk structure.",
)
defect: Defect = Field(
title="Defect Object",
description="Unit cell representation of the defect object.",
)
charge_state: Optional[int] = Field(
None,
title="Charge State",
description="Charge state of the defect.",
)
supercell_matrix: Optional[list] = Field(
None,
title="Supercell Matrix",
description="Supercell matrix used to construct the defect supercell.",
)
class DefectTaskDoc(DefectInfo, TaskDoc):
"""Defect Task Document.
Contains all the task-level information for a defect supercell calculation.
"""
@classmethod
def from_directory(
cls,
dir_name: Union[Path, str],
volumetric_files: Tuple[str, ...] = _VOLUMETRIC_FILES,
additional_fields: Optional[Dict[str, Any]] = None,
volume_change_warning_tol: float = 0.2,
defect_info_key: str = "info",
**vasp_calculation_kwargs,
) -> TaskDoc:
"""
Create a task document from a directory containing VASP files.
Parameters
----------
dir_name
The path to the folder containing the calculation outputs.
store_additional_json
Whether to store additional json files found in the calculation directory.
volumetric_files
Volumetric files to search for.
additional_fields
Dictionary of additional fields to add to output document.
volume_change_warning_tol
Maximum volume change allowed in VASP relaxations before the calculation is
tagged with a warning.
defect_info_key
The key in the `additional_json` to extract the defect information from
**vasp_calculation_kwargs
Additional parsing options that will be passed to the
:obj:`.Calculation.from_vasp_files` function.
Returns
-------
TaskDoc
A task document for the calculation.
"""
tdoc = TaskDoc.from_directory(
dir_name=dir_name,
volumetric_files=volumetric_files,
store_additional_json=True,
additional_fields=additional_fields,
volume_change_warning_tol=volume_change_warning_tol,
**vasp_calculation_kwargs,
)
return cls.from_taskdoc(tdoc, defect_info_key=defect_info_key)
@classmethod
def from_taskdoc(
cls,
taskdoc: TaskDoc,
defect_info_key: str = "info",
) -> DefectTaskDoc:
"""
Create a DefectTaskDoc from a TaskDoc
Args:
taskdoc: TaskDoc to convert
defect_info_key: The key in the `additional_json`
to extract the defect information from
Returns:
DefectTaskDoc
"""
additional_info = taskdoc.additional_json[defect_info_key]
defect = additional_info["defect"]
charge_state = additional_info["charge_state"]
defect_name = additional_info["defect_name"]
bulk_formula = additional_info["bulk_formula"]
supercell_matrix = additional_info["sc_mat"]
task_dict = taskdoc.model_dump()
task_dict.update(
{
"defect_name": defect_name,
"defect": defect,
"charge_state": charge_state,
"bulk_formula": bulk_formula,
"supercell_matrix": supercell_matrix,
}
)
return cls(**task_dict)
|
