-
Notifications
You must be signed in to change notification settings - Fork 854
/
wannier90.py
190 lines (152 loc) · 5.94 KB
/
wannier90.py
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
"""
Modules for working with wannier90 input and output.
"""
from __future__ import annotations
from typing import Sequence
import numpy as np
from scipy.io import FortranEOFError, FortranFile
__author__ = "Mark Turiansky"
__copyright__ = "Copyright 2011, The Materials Project"
__version__ = "0.1"
__maintainer__ = "Shyue Ping Ong"
__email__ = "shyuep@gmail.com"
__status__ = "Production"
__date__ = "Jun 04, 2020"
class Unk:
"""
Object representing the data in a UNK file.
.. attribute:: ik
int index of kpoint for this file
.. attribute:: data
numpy.ndarray that contains the wavefunction data for in the UNK file.
The shape should be (nbnd, ngx, ngy, ngz) for regular calculations and
(nbnd, 2, ngx, ngy, ngz) for noncollinear calculations.
.. attribute:: is_noncollinear
bool that specifies if data is from a noncollinear calculation
.. attribute:: nbnd
int number of bands in data
.. attribute:: ng
sequence of three integers that correspond to the grid size of the
given data. The definition is ng = (ngx, ngy, ngz).
"""
ik: int
is_noncollinear: bool
nbnd: int
ng: Sequence[int]
def __init__(self, ik: int, data: np.ndarray) -> None:
"""
Initialize Unk class.
Args:
ik (int): index of the kpoint UNK file is for
data (np.ndarray): data from the UNK file that has shape (nbnd,
ngx, ngy, ngz) or (nbnd, 2, ngx, ngy, ngz) if noncollinear
"""
self.ik = ik
self.data = data
@property
def data(self) -> np.ndarray:
"""
np.ndarray: contains the wavefunction data for in the UNK file.
The shape should be (nbnd, ngx, ngy, ngz) for regular calculations and
(nbnd, 2, ngx, ngy, ngz) for noncollinear calculations.
"""
return self._data
@data.setter
def data(self, value: np.ndarray) -> None:
"""
Sets the value of data.
Args:
value (np.ndarray): data to replace stored data, must haveshape
(nbnd, ngx, ngy, ngz) or (nbnd, 2, ngx, ngy, ngz) if
noncollinear calculation
"""
temp_val = np.array(value, dtype=np.complex128)
if len(temp_val.shape) not in [4, 5]:
raise ValueError(
"invalid data shape, must be (nbnd, ngx, ngy, ngz"
") or (nbnd, 2, ngx, ngy, ngz) for noncollinear "
f"data, given {temp_val.shape}"
)
if len(temp_val.shape) == 5 and temp_val.shape[1] != 2:
raise ValueError(
f"invalid noncollinear data, shape should be (nbnd, 2, ngx, ngy, ngz), given {temp_val.shape}"
)
self._data = temp_val
# derived properties
self.is_noncollinear = len(self.data.shape) == 5
self.nbnd = self.data.shape[0]
self.ng = self.data.shape[-3:]
@staticmethod
def from_file(filename: str) -> object:
"""
Reads the UNK data from file.
Args:
filename (str): path to UNK file to read
Returns:
Unk object
"""
input_data = []
with FortranFile(filename, "r") as f:
*ng, ik, nbnd = f.read_ints()
for _ in range(nbnd):
input_data.append(
# when reshaping need to specify ordering as fortran
f.read_record(np.complex128).reshape(ng, order="F")
)
try:
for _ in range(nbnd):
input_data.append(f.read_record(np.complex128).reshape(ng, order="F"))
is_noncollinear = True
except FortranEOFError:
is_noncollinear = False
# mypy made me create an extra variable here >:(
data = np.array(input_data, dtype=np.complex128)
# spinors are interwoven, need to separate them
if is_noncollinear:
temp_data = np.empty((nbnd, 2, *ng), dtype=np.complex128)
temp_data[:, 0, :, :, :] = data[::2, :, :, :]
temp_data[:, 1, :, :, :] = data[1::2, :, :, :]
return Unk(ik, temp_data)
return Unk(ik, data)
def write_file(self, filename: str) -> None:
"""
Write the UNK file.
Args:
filename (str): path to UNK file to write, the name should have the
form 'UNKXXXXX.YY' where XXXXX is the kpoint index (Unk.ik) and
YY is 1 or 2 for the spin index or NC if noncollinear
"""
with FortranFile(filename, "w") as f:
f.write_record(np.array([*self.ng, self.ik, self.nbnd], dtype=np.int32))
for ib in range(self.nbnd):
if self.is_noncollinear:
f.write_record(self.data[ib, 0].flatten("F"))
f.write_record(self.data[ib, 1].flatten("F"))
else:
f.write_record(self.data[ib].flatten("F"))
def __repr__(self) -> str:
return (
f"<UNK ik={self.ik} nbnd={self.nbnd} ncl={self.is_noncollinear}"
f" ngx={self.ng[0]} ngy={self.ng[1]} ngz={self.ng[2]}>"
)
def __eq__(self, other: object) -> bool:
if not isinstance(other, Unk):
return NotImplemented
if not np.allclose(self.ng, other.ng):
return False
if self.ik != other.ik:
return False
if self.is_noncollinear != other.is_noncollinear:
return False
if self.nbnd != other.nbnd:
return False
for ib in range(self.nbnd):
if self.is_noncollinear:
if not (
np.allclose(self.data[ib, 0], other.data[ib, 0], atol=1e-4)
and np.allclose(self.data[ib, 1], other.data[ib, 1], atol=1e-4)
):
return False
elif not np.allclose(self.data[ib], other.data[ib], atol=1e-4):
return False
return True