Test failure with spglib 1.12.2.post0
risicle opened this issue · 8 comments
Hi, we're trying to maintain seekpath packages for Nix/NixOS. When we upgraded spglib from 1.10.4.11 to 1.12.2.post0 we noticed that a single test in seekpath 1.8.4, test_oI2Y started failing. The error being:
======================================================================
FAIL: test_oI2Y (seekpath.test_paths_hpkot.TestPaths3D_HPKOT)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/build/seekpath-1.8.4/seekpath/test_paths_hpkot.py", line 706, in test_oI2Y
self.base_test(ext_bravais="oI2", with_inv=True)
File "/build/seekpath-1.8.4/seekpath/test_paths_hpkot.py", line 366, in base_test
self.assertEqual(res['bravais_lattice_extended'], ext_bravais)
AssertionError: 'oI3' != 'oI2'
- oI3
? ^
+ oI2
? ^
Same error on python 2.7 & 3.7, on macos & linux.
Thanks for the report!
Indeed I can reproduce the error.
Last version that works: spglib==1.11.2.post1
First version that fails: spglib==1.12.0.post5
Minimal example to reproduce:
import numpy as np
import json
class NumpyEncoder(json.JSONEncoder):
def default(self, obj):
if isinstance(obj, np.ndarray):
return obj.tolist()
return json.JSONEncoder.default(self, obj)
def test_oI2Y():
"""
Obtain the k-path for a test system with inversion symmetry and
Bravais lattice (extended) oI2.
"""
import spglib
from seekpath import hpkot
system = (
[
[8.186532843027958, 0.0, 0.0],
[0.0, 5.827100673574356, 0.0],
[0.0, 0.0, 5.8365707664294835]
], [
[0.2905378000000001, 0.0, 0.0],
[0.2094621999999999, 0.0, 0.5],
[0.2094621999999999, 0.5, 0.5],
[0.7905378000000001, 0.0, 0.5],
[0.0, 0.75, 0.1751481400000001],
[0.5, 0.75, 0.32485186],
[0.7905378000000001, 0.5, 0.5],
[0.7094621999999999, 0.5, 0.0],
[0.7094621999999999, 0.0, 0.0],
[0.2905378, 0.5, 0.0],
[0.5, 0.25, 0.6751481400000001],
[0.0, 0.25, 0.8248518599999999],
[0.0, 0.75, 0.7411616600000002],
[0.5, 0.75, 0.7588383399999998],
[0.5, 0.25, 0.2411616600000002],
[0.0, 0.25, 0.2588383399999998],
[0.25, 0.75, 0.25],
[0.25, 0.25, 0.75],
[0.75, 0.25, 0.75],
[0.75, 0.75, 0.25]
],
[8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8,
8, 38, 38, 38, 38, 72, 72, 72, 72])
sym_ds = spglib.get_symmetry_dataset(system)
print(json.dumps(sym_ds, indent=2, sort_keys=True, cls=NumpyEncoder))
res = hpkot.get_path(system, with_time_reversal=False)
assert res['bravais_lattice_extended'] == 'oI2'
if __name__ == "__main__":
test_oI2Y()I also report the output of the code (in particular, the json-serialized get_symmetry_dataset for the two versions):
- output-ok.txt [for the working version reported above]
- output-failure.txt [for the failing version reported above]
In particular, the main issue is that in the "working" version, we have from spglib:
"std_lattice": [
[8.186532843027958, 0.0, 0.0],
[0.0, 5.827100673574356, 0.0],
[0.0, 0.0, 5.8365707664294835]
]
while in the "failing" version:
"std_lattice": [
[5.827100673574355, 0.0, 0.0],
[0.0, 8.186532843027958, 0.0],
[0.0, 0.0, 5.8365707664294835]
]
and since the order is different, the categorisation (2 vs. 3) by seek path is different.
I will investigate with the author of spglib.
I am the author of spglib. This is probably due to spglib. oI2 or oI3 may be undetermined by the current implementation. So a detailed change introduced recently changed the choice. But this choice may/should be able to be determined. I will look at it deeper and get back here when I can resolve this issue.
Thanks a lot @atztogo!
In orthorhombic system, I found four space group types, Cmma (67), Ccca(68), Ibca(73), Imma(74), were wrongly treated. They were exceptions than my previous definitions, i.e., my understanding on crystallography was not enough. This fix is in the develop branch (atztogo/spglib@c61d109). Previously degrees of freedom of a,b,c choice relied on number of hall symbols for each space group type. But now, degrees of freedom of a, b, c choice rely on the index of L(g) in N_\epsilon(g) of highest symmetry or equivalently the index of L(g) in N_A(g) (ITA 2016, 3.5. Normalizers of space groups and their use in crystallography).
The similar problem may exist in monoclinic system. I will work on it and once it will be solved, I will make a spglib release.
I have released spglib-1.13.0 with the fix above. For monoclinic system, I made small update, but not like the orthorhombic case above. This version is better for the standardization.
Hi @atztogo thanks!
I'm starting to prepare a new version of seekpath pointing to the new version of spglib.
A question: do you agree, then, that there is no oI space group with inversion symmetry that can have a being the largest vector (a>b and a>c)?
The four space groups with oI and inversion symmetry are:
- 71: Immm
- 72: Ibam
- 73: Ibca
- 74: Imma
For sure in 71 and 74 we always apply a<b. This is also the case for 72 and 73, right?
(And in the case of oI without inversion symmetry, instead, this is possible because there is space group Ima2 so the order of the three vectors is fixed by the symmetry, and we do not have freedom to choose their ordering, right?)
Yes, most strictly, they are implemented as follows.
71: Immm, a < b + 1e-10, b < c + 1e-10
72: Ibam, a < b + 1e-10
73: Ibca, a < b + 1e-10, b < c + 1e-10
74: Imma, a < b + 1e-10
For Ima2, yes, it is fixed by symmetry. The fact that you wrote in the parenthesis is correct for 3D crystal. But I can't explain the reason in short works. It is not the matter of centring or inversion symmetry. Non-symmorphic operations make thing tricky. I just relied on the data base of affine normalizer to see how many degrees of freedom exist. Pbca is tricky. We have choices abc, bca, cab, but flip of two axies is not allowed. For this, I implement
61: Pbca, a < b + 1e-10, a < c + 1e-10.
Fixed in release v1.9.0 (in particular, in commit a130478)