create a hcp mg grain boundary mgΣ7[0001](0001) too many values to unpack (expected 3)

[TongaoY]

Python version

Python3.10

Pymatgen version

2024.3.1

Operating system version

ubuntu22.04-py310-torch2.1.2-tf2.14.0-1.13.1

Current behavior

from pymatgen.core import Structure, Element
from pymatgen.analysis.gb.grain import GrainBoundary, GrainBoundaryGenerator

angle = GrainBoundaryGenerator.get_rotation_angle_from_sigma(7,[0,0,0,1], lat_type='H',ratio=None)
struc = Structure.from_file("mg.cif")
generator = GrainBoundaryGenerator(struc)
gb = generator.gb_from_parameters(
rotation_axis=[0,0,0,1],
rotation_angle=angle[0],
expand_times=8,
vacuum_thickness=0.0,
plane=None,
)
gb.to(filename="Mg_GB.cif")

---

ValueError Traceback (most recent call last)
Cell In[19], line 10
8 generator = GrainBoundaryGenerator(struc)
9 #gb = generator.gb_from_parameters([0,0,0,1],angle[0], plane = None, expand_times=8, vacuum_thickness=0.0)
---> 10 gb = generator.gb_from_parameters(
11 rotation_axis=[0,0,0,1], # 旋转轴向量，应为长度为3的列表
12 rotation_angle=angle[0], # 旋转角度，假设 angle 已经定义并包含所需角度
13 expand_times=8, # 扩展次数
14 vacuum_thickness=0.0, # 真空厚度
15 plane=None, # 平面信息
16 )
17 gb.to(filename="Mg_GB.cif")

File /opt/conda/lib/python3.10/site-packages/pymatgen/analysis/gb/grain.py:567, in GrainBoundaryGenerator.gb_from_parameters(self, rotation_axis, rotation_angle, expand_times, vacuum_thickness, ab_shift, normal, ratio, plane, max_search, tol_coi, rm_ratio, quick_gen)
564 index = reduce(gcd, plane)
565 plane = [int(round(x / index)) for x in plane]
--> 567 t1, t2 = self.get_trans_mat(
568 r_axis=rotation_axis,
569 angle=rotation_angle,
570 normal=normal,
571 trans_cry=trans_cry,
572 lat_type=lat_type,
573 ratio=ratio,
574 surface=plane,
575 max_search=max_search,
576 quick_gen=quick_gen,
577 )
579 # find the join_plane
580 if lat_type.lower() != "c":

File /opt/conda/lib/python3.10/site-packages/pymatgen/analysis/gb/grain.py:1110, in GrainBoundaryGenerator.get_trans_mat(r_axis, angle, normal, trans_cry, lat_type, ratio, surface, max_search, quick_gen)
1108 r_matrix = (np.array(r_list) / com_fac / sigma).reshape(3, 3)
1109 else:
-> 1110 u, v, w = r_axis
1111 if lat_type.lower() == "c":
1112 mu = 1

ValueError: too many values to unpack (expected 3)

Expected Behavior

generate gbs

Minimal example

No response

Relevant files to reproduce this bug

No response

[shyuep]

You need to use the 3-integer specification of the rotation axis. Not 4. In hexagonal structures, one of the indices (the third) is redundant.

[TongaoY]

You need to use the 3-integer specification of the rotation axis. Not 4. In hexagonal structures, one of the indices (the third) is redundant.
when I change code as you say:
from pymatgen.core import Structure, Element
from pymatgen.analysis.gb.grain import GrainBoundary, GrainBoundaryGenerator
#找到给定西格玛值的所有可能的旋转角度。
angle = GrainBoundaryGenerator.get_rotation_angle_from_sigma(7, [0, 0, 0, 1], lat_type='h')

struc = Structure.from_file("mg.cif")
generator = GrainBoundaryGenerator(struc)
gb = generator.gb_from_parameters(
[0,0,1],angle[0],
expand_times=4,
vacuum_thickness=1.0,
plane=None
)

gb.to(filename="Mg_GB.cif")

It turns a new wrong:

RuntimeError Traceback (most recent call last)
Cell In[4], line 8
6 struc = Structure.from_file("mg.cif")
7 generator = GrainBoundaryGenerator(struc)
----> 8 gb = generator.gb_from_parameters(
9 [0,0,1],21.79,
10 expand_times=4,
11 vacuum_thickness=1.0,
12 plane=None
13 )
14 #gb = generator.gb_from_parameters([[1, 0, -1, 0], rotation_angle,angle[0],plane=[1,-2,1,4] , expand_times=4,vacuum_thickness=1.0)
15 gb.to(filename="Mg_GB.cif")

File /opt/conda/lib/python3.10/site-packages/pymatgen/analysis/gb/grain.py:567, in GrainBoundaryGenerator.gb_from_parameters(self, rotation_axis, rotation_angle, expand_times, vacuum_thickness, ab_shift, normal, ratio, plane, max_search, tol_coi, rm_ratio, quick_gen)
564 index = reduce(gcd, plane)
565 plane = [int(round(x / index)) for x in plane]
--> 567 t1, t2 = self.get_trans_mat(
568 r_axis=rotation_axis,
569 angle=rotation_angle,
570 normal=normal,
571 trans_cry=trans_cry,
572 lat_type=lat_type,
573 ratio=ratio,
574 surface=plane,
575 max_search=max_search,
576 quick_gen=quick_gen,
577 )
579 # find the join_plane
580 if lat_type.lower() != "c":

File /opt/conda/lib/python3.10/site-packages/pymatgen/analysis/gb/grain.py:1202, in GrainBoundaryGenerator.get_trans_mat(r_axis, angle, normal, trans_cry, lat_type, ratio, surface, max_search, quick_gen)
1199 r_matrix = (np.array(r_list) / com_fac / sigma).reshape(3, 3)
1201 if sigma > 1000:
-> 1202 raise RuntimeError("Sigma >1000 too large. Are you sure what you are doing, Please check the GB if exist")
1203 # transform surface, r_axis, r_matrix in terms of primitive lattice
1204 surface = np.matmul(surface, np.transpose(trans_cry))

RuntimeError: Sigma >1000 too large. Are you sure what you are doing, Please check the GB if exist

But

exist