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
|
from typing import List, Optional
from pydantic import Field
from emmet.core.material_property import PropertyDoc
import numpy as np
from emmet.core.mpid import MPID
from pymatgen.core import Structure
class AbsorptionDoc(PropertyDoc):
"""Absorption spectrum based on frequency dependent dielectric function calculations."""
property_name: str = "Optical absorption spectrum"
task_id: str = Field(..., description="Calculation id")
energies: List[float] = Field(
..., description="Absorption energy in eV starting from 0"
)
energy_max: float = Field(..., description="Maximum energy")
absorption_coefficient: List[float] = Field(
..., description="Absorption coefficient in cm^-1"
)
average_imaginary_dielectric: List[float] = Field(
...,
description="Imaginary part of the dielectric function corresponding to the "
"energies",
)
average_real_dielectric: List[float] = Field(
...,
description="Real part of the dielectric function corresponding to the energies",
)
bandgap: Optional[float] = Field(None, description="The electronic band gap")
nkpoints: Optional[float] = Field(
None, description="The number of kpoints used in the calculation"
)
@classmethod
def _convert_list_to_tensor(cls, l):
l = np.array(l)
a = np.array([[l[0], l[3], l[4]], [l[3], l[1], l[5]], [l[4], l[5], l[2]]])
return a
@classmethod
def from_structure(
cls,
material_id: MPID,
energies: List,
task_id: str,
real_d: List[np.ndarray],
imag_d: List[np.ndarray],
absorption_co: List,
bandgap: float,
structure: Structure,
nkpoints: float,
**kwargs,
):
real_d_average = [
np.average(np.diagonal(cls._convert_list_to_tensor(t))) for t in real_d
]
imag_d_average = [
np.average(np.diagonal(cls._convert_list_to_tensor(t))) for t in imag_d
]
absorption_co = list(np.array(absorption_co))
energy_max = np.array(energies).max()
return super().from_structure(
meta_structure=structure,
material_id=material_id,
**{
"energies": energies,
"energy_max": energy_max,
"absorption_coefficient": absorption_co,
"average_imaginary_dielectric": imag_d_average,
"average_real_dielectric": real_d_average,
"bandgap": bandgap,
"nkpoints": nkpoints,
"task_id": task_id,
},
**kwargs,
)
|
