4075885785

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Committed by Shyue Ping Ong

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Merge branch 'master' of github.com:materialsproject/pymatgen

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98.11

/pymatgen/symmetry/tests/test_settings.py

1	from __future__ import annotations	1✔
2
3	import unittest	1✔
4
5	import numpy as np	1✔
6
7	from pymatgen.symmetry.settings import JonesFaithfulTransformation, Lattice, SymmOp	1✔
8
9	__author__ = "Matthew Horton"	1✔
10	__copyright__ = "Copyright 2017, The Materials Project"	1✔
11	__version__ = "0.1"	1✔
12	__maintainer__ = "Matthew Horton"	1✔
13	__email__ = "mkhorton@lbl.gov"	1✔
14	__status__ = "Development"	1✔
15	__date__ = "Apr 2017"	1✔
16
17
18	class JonesFaithfulTransformationTest(unittest.TestCase):	1✔
19	def setUp(self):	1✔
20	self.test_strings = [	1✔
21	"a,b,c;0,0,0", # identity
22	"a-b,a+b,2c;0,0,1/2",
23	"a/4+b/4-c/2,a/4-b/4,-a/2-b/2;0,0,0",
24	"a,b,c;1/4,1/2,3/4",
25	] # pure translation
26	self.test_Pps = [	1✔
27	([[1, 0, 0], [0, 1, 0], [0, 0, 1]], [0, 0, 0]),
28	([[1, 1, 0], [-1, 1, 0], [0, 0, 2]], [0, 0, 0.5]),
29	([[0.25, 0.25, -0.5], [0.25, -0.25, -0.5], [-0.5, 0, 0]], [0, 0, 0]),
30	([[1, 0, 0], [0, 1, 0], [0, 0, 1]], [0.25, 0.5, 0.75]),
31	]
32
33	def test_init(self):	1✔
34	for test_string, test_Pp in zip(self.test_strings, self.test_Pps):	1✔
35	jft = JonesFaithfulTransformation.from_transformation_string(test_string)	1✔
36	jft2 = JonesFaithfulTransformation(test_Pp[0], test_Pp[1])	1✔
37	assert np.allclose(jft.P, jft2.P)	1✔
38	assert np.allclose(jft.p, jft2.p)	1✔
39	assert test_string == jft.transformation_string	1✔
40	assert test_string == jft2.transformation_string	1✔
41
42	def test_inverse(self):	1✔
43	for test_string in self.test_strings:	1✔
44	jft = JonesFaithfulTransformation.from_transformation_string(test_string)	1✔
45	assert jft == jft.inverse.inverse	1✔
46	assert jft.transformation_string == jft.inverse.inverse.transformation_string	1✔
47
48	def test_transform_lattice(self):	1✔
49	lattice = Lattice.cubic(5)	1✔
50
51	all_ref_lattices = [	1✔
52	[[5.0, 0.0, 0.0], [0.0, 5.0, 0.0], [0.0, 0.0, 5.0]],
53	[[5.0, 5.0, 0.0], [-5.0, 5.0, 0.0], [0.0, 0.0, 10.0]],
54	[[1.25, 1.25, -2.5], [1.25, -1.25, -2.5], [-2.5, 0.0, 0.0]],
55	[[5.0, 0.0, 0.0], [0.0, 5.0, 0.0], [0.0, 0.0, 5.0]],
56	]
57
58	for ref_lattice, (P, p) in zip(all_ref_lattices, self.test_Pps):	1✔
59	jft = JonesFaithfulTransformation(P, p)	1✔
60	assert np.allclose(jft.transform_lattice(lattice).matrix, ref_lattice)	1✔
61
62	def test_transform_coords(self):	1✔
63	coords = [[0, 0, 0], [0.5, 0.5, 0.5]]	1✔
64
65	all_ref_coords = [	1✔
66	[[0.0, 0.0, 0.0], [0.5, 0.5, 0.5]],
67	[[0.0, 0.0, -0.25], [0.0, 0.5, 0.0]],
68	[[0.0, 0.0, 0.0], [-1.0, 0.0, -1.5]],
69	[[-0.25, -0.5, -0.75], [0.25, 0.0, -0.25]],
70	]
71
72	for ref_coords, (P, p) in zip(all_ref_coords, self.test_Pps):	1✔
73	jft = JonesFaithfulTransformation(P, p)	1✔
74	transformed_coords = jft.transform_coords(coords)	1✔
75	for coord, ref_coord in zip(transformed_coords, ref_coords):	1✔
76	assert np.allclose(coord, ref_coord)	1✔
77
78	def test_transform_symmops(self):	1✔
79	# reference data for this test taken from GENPOS
80	# http://cryst.ehu.es/cryst/get_gen.html
81
82	# Fm-3m
83	input_symmops = """x,y,z	1✔
84	-x,-y,z
85	-x,y,-z
86	x,-y,-z
87	z,x,y
88	z,-x,-y
89	-z,-x,y
90	-z,x,-y
91	y,z,x
92	-y,z,-x
93	y,-z,-x
94	-y,-z,x
95	y,x,-z
96	-y,-x,-z
97	y,-x,z
98	-y,x,z
99	x,z,-y
100	-x,z,y
101	-x,-z,-y
102	x,-z,y
103	z,y,-x
104	z,-y,x
105	-z,y,x
106	-z,-y,-x
107	-x,-y,-z
108	x,y,-z
109	x,-y,z
110	-x,y,z
111	-z,-x,-y
112	-z,x,y
113	z,x,-y
114	z,-x,y
115	-y,-z,-x
116	y,-z,x
117	-y,z,x
118	y,z,-x
119	-y,-x,z
120	y,x,z
121	-y,x,-z
122	y,-x,-z
123	-x,-z,y
124	x,-z,-y
125	x,z,y
126	-x,z,-y
127	-z,-y,x
128	-z,y,-x
129	z,-y,-x
130	z,y,x"""
131
132	# Fm-3m transformed by (a-b,a+b,2c;0,0,1/2)
133	ref_transformed_symmops = """x,y,z	1✔
134	-x,-y,z
135	-y,-x,-z+1/2
136	y,x,-z+1/2
137	-1/2x-1/2y+z+1/4,1/2x+1/2y+z+1/4,-1/2x+1/2y+3/4
138	1/2x+1/2y+z+1/4,-1/2x-1/2y+z+1/4,1/2x-1/2y+3/4
139	1/2x+1/2y-z+3/4,-1/2x-1/2y-z+3/4,-1/2x+1/2y+3/4
140	-1/2x-1/2y-z+3/4,1/2x+1/2y-z+3/4,1/2x-1/2y+3/4
141	-1/2x+1/2y-z+3/4,-1/2x+1/2y+z+1/4,1/2x+1/2y+3/4
142	1/2x-1/2y-z+3/4,1/2x-1/2y+z+1/4,-1/2x-1/2y+3/4
143	-1/2x+1/2y+z+1/4,-1/2x+1/2y-z+3/4,-1/2x-1/2y+3/4
144	1/2x-1/2y+z+1/4,1/2x-1/2y-z+3/4,1/2x+1/2y+3/4
145	-x,y,-z+1/2
146	x,-y,-z+1/2
147	y,-x,z
148	-y,x,z
149	1/2x+1/2y-z+3/4,1/2x+1/2y+z+1/4,1/2x-1/2y+3/4
150	-1/2x-1/2y-z+3/4,-1/2x-1/2y+z+1/4,-1/2x+1/2y+3/4
151	-1/2x-1/2y+z+1/4,-1/2x-1/2y-z+3/4,1/2x-1/2y+3/4
152	1/2x+1/2y+z+1/4,1/2x+1/2y-z+3/4,-1/2x+1/2y+3/4
153	1/2x-1/2y+z+1/4,-1/2x+1/2y+z+1/4,-1/2x-1/2y+3/4
154	-1/2x+1/2y+z+1/4,1/2x-1/2y+z+1/4,1/2x+1/2y+3/4
155	1/2x-1/2y-z+3/4,-1/2x+1/2y-z+3/4,1/2x+1/2y+3/4
156	-1/2x+1/2y-z+3/4,1/2x-1/2y-z+3/4,-1/2x-1/2y+3/4
157	-x,-y,-z+1/2
158	x,y,-z+1/2
159	y,x,z
160	-y,-x,z
161	1/2x+1/2y-z+3/4,-1/2x-1/2y-z+3/4,1/2x-1/2y+3/4
162	-1/2x-1/2y-z+3/4,1/2x+1/2y-z+3/4,-1/2x+1/2y+3/4
163	-1/2x-1/2y+z+1/4,1/2x+1/2y+z+1/4,1/2x-1/2y+3/4
164	1/2x+1/2y+z+1/4,-1/2x-1/2y+z+1/4,-1/2x+1/2y+3/4
165	1/2x-1/2y+z+1/4,1/2x-1/2y-z+3/4,-1/2x-1/2y+3/4
166	-1/2x+1/2y+z+1/4,-1/2x+1/2y-z+3/4,1/2x+1/2y+3/4
167	1/2x-1/2y-z+3/4,1/2x-1/2y+z+1/4,1/2x+1/2y+3/4
168	-1/2x+1/2y-z+3/4,-1/2x+1/2y+z+1/4,-1/2x-1/2y+3/4
169	x,-y,z
170	-x,y,z
171	-y,x,-z+1/2
172	y,-x,-z+1/2
173	-1/2x-1/2y+z+1/4,-1/2x-1/2y-z+3/4,-1/2x+1/2y+3/4
174	1/2x+1/2y+z+1/4,1/2x+1/2y-z+3/4,1/2x-1/2y+3/4
175	1/2x+1/2y-z+3/4,1/2x+1/2y+z+1/4,-1/2x+1/2y+3/4
176	-1/2x-1/2y-z+3/4,-1/2x-1/2y+z+1/4,1/2x-1/2y+3/4
177	-1/2x+1/2y-z+3/4,1/2x-1/2y-z+3/4,1/2x+1/2y+3/4
178	1/2x-1/2y-z+3/4,-1/2x+1/2y-z+3/4,-1/2x-1/2y+3/4
179	-1/2x+1/2y+z+1/4,1/2x-1/2y+z+1/4,-1/2x-1/2y+3/4
180	1/2x-1/2y+z+1/4,-1/2x+1/2y+z+1/4,1/2x+1/2y+3/4"""
181
182	jft = JonesFaithfulTransformation.from_transformation_string(self.test_strings[1])	1✔
183
184	input_symmops = [SymmOp.from_xyz_string(s) for s in input_symmops.split()]	1✔
185	ref_transformed_symmops = [SymmOp.from_xyz_string(s) for s in ref_transformed_symmops.split()]	1✔
186
187	transformed_symmops = [jft.transform_symmop(op) for op in input_symmops]	1✔
188
189	for transformed_op, ref_transformed_op in zip(transformed_symmops, ref_transformed_symmops):	1✔
190	assert transformed_op == ref_transformed_op	1✔
191
192
193	if __name__ == "__main__":	1✔
194	unittest.main()	×

materialsproject / pymatgen / 4075885785

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