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/pymatgen/symmetry/tests/test_maggroups.py

from __future__ import annotations

import unittest

import numpy as np

from pymatgen.core.lattice import Lattice
from pymatgen.symmetry.groups import SpaceGroup
from pymatgen.symmetry.maggroups import MagneticSpaceGroup
from pymatgen.util.testing import PymatgenTest

__author__ = "Matthew Horton"
__copyright__ = "Copyright 2017, The Materials Project"
__version__ = "0.1"
__maintainer__ = "Matthew Horton"
__email__ = "mkhorton@lbl.gov"
__status__ = "Beta"
__date__ = "Feb 2017"


class MagneticSpaceGroupTest(PymatgenTest):
    def setUp(self):
        self.msg_1 = MagneticSpaceGroup([70, 530])
        self.msg_2 = MagneticSpaceGroup([62, 448])
        self.msg_3 = MagneticSpaceGroup([20, 37])
        self.msg_4 = MagneticSpaceGroup([2, 7], "c,1/4a+1/4b,-1/2a+1/2b;0,0,0")

    def test_init(self):
        # test init with the following space group:
        # 71.538 (BNS number), I_cmmm (BNS label)
        # 65.10.554 (same space group as above, OG number), C_Immm (OG label)
        msg_from_bns_1 = MagneticSpaceGroup("I_cmmm")
        msg_from_bns_2 = MagneticSpaceGroup([71, 538])
        msg_from_og_1 = MagneticSpaceGroup.from_og("C_Immm")
        msg_from_og_2 = MagneticSpaceGroup.from_og([65, 10, 554])
        assert msg_from_bns_1 == msg_from_bns_2
        assert msg_from_og_1 == msg_from_og_2
        assert msg_from_bns_1 == msg_from_og_1

    def test_crystal_system(self):
        assert self.msg_1.crystal_system == "orthorhombic"
        assert self.msg_2.crystal_system == "orthorhombic"
        assert self.msg_3.crystal_system == "orthorhombic"

    def test_sg_symbol(self):
        assert self.msg_1.sg_symbol == "Fd'd'd"
        assert self.msg_2.sg_symbol == "Pn'ma'"
        assert self.msg_3.sg_symbol == "C_A222_1"

    def test_is_compatible(self):
        cubic = Lattice.cubic(1)
        hexagonal = Lattice.hexagonal(1, 2)
        rhom = Lattice.rhombohedral(3, 80)
        tet = Lattice.tetragonal(1, 2)
        ortho = Lattice.orthorhombic(1, 2, 3)
        msg = MagneticSpaceGroup("Fm-3m")
        assert msg.is_compatible(cubic)
        assert not msg.is_compatible(hexagonal)
        msg = MagneticSpaceGroup("Pnma")
        assert msg.is_compatible(cubic)
        assert msg.is_compatible(tet)
        assert msg.is_compatible(ortho)
        assert not msg.is_compatible(rhom)
        assert not msg.is_compatible(hexagonal)
        msg = MagneticSpaceGroup("P2/c")
        assert msg.is_compatible(cubic)
        assert msg.is_compatible(tet)
        assert msg.is_compatible(ortho)
        assert not msg.is_compatible(rhom)
        assert not msg.is_compatible(hexagonal)
        msg = MagneticSpaceGroup("P-1")
        assert msg.is_compatible(cubic)
        assert msg.is_compatible(tet)
        assert msg.is_compatible(ortho)
        assert msg.is_compatible(rhom)
        assert msg.is_compatible(hexagonal)

    def test_symmetry_ops(self):
        msg_1_symmops = "\n".join(map(str, self.msg_1.symmetry_ops))
        msg_1_symmops_ref = """x, y, z, +1
-x+3/4, -y+3/4, z, +1
-x, -y, -z, +1
x+1/4, y+1/4, -z, +1
x, -y+3/4, -z+3/4, -1
-x+3/4, y, -z+3/4, -1
-x, y+1/4, z+1/4, -1
x+1/4, -y, z+1/4, -1
x, y+1/2, z+1/2, +1
-x+3/4, -y+5/4, z+1/2, +1
-x, -y+1/2, -z+1/2, +1
x+1/4, y+3/4, -z+1/2, +1
x, -y+5/4, -z+5/4, -1
-x+3/4, y+1/2, -z+5/4, -1
-x, y+3/4, z+3/4, -1
x+1/4, -y+1/2, z+3/4, -1
x+1/2, y, z+1/2, +1
-x+5/4, -y+3/4, z+1/2, +1
-x+1/2, -y, -z+1/2, +1
x+3/4, y+1/4, -z+1/2, +1
x+1/2, -y+3/4, -z+5/4, -1
-x+5/4, y, -z+5/4, -1
-x+1/2, y+1/4, z+3/4, -1
x+3/4, -y, z+3/4, -1
x+1/2, y+1/2, z, +1
-x+5/4, -y+5/4, z, +1
-x+1/2, -y+1/2, -z, +1
x+3/4, y+3/4, -z, +1
x+1/2, -y+5/4, -z+3/4, -1
-x+5/4, y+1/2, -z+3/4, -1
-x+1/2, y+3/4, z+1/4, -1
x+3/4, -y+1/2, z+1/4, -1"""
        self.assertStrContentEqual(msg_1_symmops, msg_1_symmops_ref)

        msg_2_symmops = "\n".join(map(str, self.msg_2.symmetry_ops))
        msg_2_symmops_ref = """x, y, z, +1
-x, y+1/2, -z, +1
-x, -y, -z, +1
x, -y+1/2, z, +1
x+1/2, -y+1/2, -z+1/2, -1
-x+1/2, -y, z+1/2, -1
-x+1/2, y+1/2, z+1/2, -1
x+1/2, y, -z+1/2, -1"""
        self.assertStrContentEqual(msg_2_symmops, msg_2_symmops_ref)

        msg_3_symmops = "\n".join(map(str, self.msg_3.symmetry_ops))
        msg_3_symmops_ref = """x, y, z, +1
x, -y, -z, +1
-x, y, -z+1/2, +1
-x, -y, z+1/2, +1
x, y+1/2, z+1/2, -1
x+1/2, -y, -z+1/2, -1
-x+1/2, y, -z, -1
-x+1/2, -y, z, -1
x+1/2, y+1/2, z, +1
x+1/2, -y+1/2, -z, +1
-x+1/2, y+1/2, -z+1/2, +1
-x+1/2, -y+1/2, z+1/2, +1
x+1/2, y, z+1/2, -1
x, -y+1/2, -z+1/2, -1
-x, y+1/2, -z, -1
-x, -y+1/2, z, -1"""
        assert msg_3_symmops == msg_3_symmops_ref

        msg_4_symmops = "\n".join(map(str, self.msg_4.symmetry_ops))
        msg_4_symmops_ref = """x, y, z, +1
-x, -y, -z, +1
x+1/2, y, z, -1
-x+1/2, -y, -z, -1"""
        assert msg_4_symmops == msg_4_symmops_ref

    def test_equivalence_to_spacegroup(self):
        # first 230 magnetic space groups have same symmetry operations
        # as normal space groups, so should give same orbits

        labels = ["Fm-3m", "Pnma", "P2/c", "P-1"]

        points = [[0, 0, 0], [0.5, 0, 0], [0.11, 0.22, 0.33]]

        for label in labels:
            sg = SpaceGroup(label)
            msg = MagneticSpaceGroup(label)
            assert sg.crystal_system == msg.crystal_system
            for p in points:
                pp_sg = np.array(sg.get_orbit(p))
                pp_msg = np.array(msg.get_orbit(p, 0)[0])  # discarding magnetic moment information
                pp_sg = pp_sg[np.lexsort(np.transpose(pp_sg)[::-1])]  # sorting arrays so we can compare them
                pp_msg = pp_msg[np.lexsort(np.transpose(pp_msg)[::-1])]
                assert np.allclose(pp_sg, pp_msg)

    def test_str(self):
        msg = MagneticSpaceGroup([4, 11])

        ref_string = """BNS: 4.11 P_b2_1
Operators: (1|0,0,0) (2y|0,1/2,0) (1|0,1/2,0)' (2y|0,0,0)'
Wyckoff Positions:
4e  (x,y,z;mx,my,mz) (-x,y+1/2,-z;-mx,my,-mz) (x,y+1/2,z;-mx,-my,-mz)
    (-x,y,-z;mx,-my,mz)
2d  (1/2,y,1/2;mx,0,mz) (1/2,y+1/2,1/2;-mx,0,-mz)
2c  (1/2,y,0;mx,0,mz) (1/2,y+1/2,0;-mx,0,-mz)
2b  (0,y,1/2;mx,0,mz) (0,y+1/2,1/2;-mx,0,-mz)
2a  (0,y,0;mx,0,mz) (0,y+1/2,0;-mx,0,-mz)
Alternative OG setting exists for this space group."""

        ref_string_all = """BNS: 4.11 P_b2_1                OG: 3.7.14 P_2b2'
OG-BNS Transform: (a,2b,c;0,0,0)
Operators (BNS): (1|0,0,0) (2y|0,1/2,0) (1|0,1/2,0)' (2y|0,0,0)'
Wyckoff Positions (BNS):
4e  (x,y,z;mx,my,mz) (-x,y+1/2,-z;-mx,my,-mz) (x,y+1/2,z;-mx,-my,-mz)
    (-x,y,-z;mx,-my,mz)
2d  (1/2,y,1/2;mx,0,mz) (1/2,y+1/2,1/2;-mx,0,-mz)
2c  (1/2,y,0;mx,0,mz) (1/2,y+1/2,0;-mx,0,-mz)
2b  (0,y,1/2;mx,0,mz) (0,y+1/2,1/2;-mx,0,-mz)
2a  (0,y,0;mx,0,mz) (0,y+1/2,0;-mx,0,-mz)
Operators (OG): (1|0,0,0) (2y|0,1,0) (1|0,1,0)' (2y|0,0,0)'
Wyckoff Positions (OG): (1,0,0)+ (0,2,0)+ (0,0,1)+
4e  (x,y,z;mx,my,mz) (-x,y+1,-z;-mx,my,-mz) (x,y+1,z;-mx,-my,-mz)
    (-x,y,-z;mx,-my,mz)
2d  (1/2,y,1/2;mx,0,mz) (-1/2,y+1,-1/2;-mx,0,-mz)
2c  (1/2,y,0;mx,0,mz) (-1/2,y+1,0;-mx,0,-mz)
2b  (0,y,1/2;mx,0,mz) (0,y+1,-1/2;-mx,0,-mz)
2a  (0,y,0;mx,0,mz) (0,y+1,0;-mx,0,-mz)"""

        self.assertStrContentEqual(str(msg), ref_string)
        self.assertStrContentEqual(msg.data_str(), ref_string_all)


if __name__ == "__main__":
    unittest.main()

1	from __future__ import annotations	1✔
2
3	import unittest	1✔
4
5	import numpy as np	1✔
6
7	from pymatgen.core.lattice import Lattice	1✔
8	from pymatgen.symmetry.groups import SpaceGroup	1✔
9	from pymatgen.symmetry.maggroups import MagneticSpaceGroup	1✔
10	from pymatgen.util.testing import PymatgenTest	1✔
11
12	__author__ = "Matthew Horton"	1✔
13	__copyright__ = "Copyright 2017, The Materials Project"	1✔
14	__version__ = "0.1"	1✔
15	__maintainer__ = "Matthew Horton"	1✔
16	__email__ = "mkhorton@lbl.gov"	1✔
17	__status__ = "Beta"	1✔
18	__date__ = "Feb 2017"	1✔
19
20
21	class MagneticSpaceGroupTest(PymatgenTest):	1✔
22	def setUp(self):	1✔
23	self.msg_1 = MagneticSpaceGroup([70, 530])	1✔
24	self.msg_2 = MagneticSpaceGroup([62, 448])	1✔
25	self.msg_3 = MagneticSpaceGroup([20, 37])	1✔
26	self.msg_4 = MagneticSpaceGroup([2, 7], "c,1/4a+1/4b,-1/2a+1/2b;0,0,0")	1✔
27
28	def test_init(self):	1✔
29	# test init with the following space group:
30	# 71.538 (BNS number), I_cmmm (BNS label)
31	# 65.10.554 (same space group as above, OG number), C_Immm (OG label)
32	msg_from_bns_1 = MagneticSpaceGroup("I_cmmm")	1✔
33	msg_from_bns_2 = MagneticSpaceGroup([71, 538])	1✔
34	msg_from_og_1 = MagneticSpaceGroup.from_og("C_Immm")	1✔
35	msg_from_og_2 = MagneticSpaceGroup.from_og([65, 10, 554])	1✔
36	assert msg_from_bns_1 == msg_from_bns_2	1✔
37	assert msg_from_og_1 == msg_from_og_2	1✔
38	assert msg_from_bns_1 == msg_from_og_1	1✔
39
40	def test_crystal_system(self):	1✔
41	assert self.msg_1.crystal_system == "orthorhombic"	1✔
42	assert self.msg_2.crystal_system == "orthorhombic"	1✔
43	assert self.msg_3.crystal_system == "orthorhombic"	1✔
44
45	def test_sg_symbol(self):	1✔
46	assert self.msg_1.sg_symbol == "Fd'd'd"	1✔
47	assert self.msg_2.sg_symbol == "Pn'ma'"	1✔
48	assert self.msg_3.sg_symbol == "C_A222_1"	1✔
49
50	def test_is_compatible(self):	1✔
51	cubic = Lattice.cubic(1)	1✔
52	hexagonal = Lattice.hexagonal(1, 2)	1✔
53	rhom = Lattice.rhombohedral(3, 80)	1✔
54	tet = Lattice.tetragonal(1, 2)	1✔
55	ortho = Lattice.orthorhombic(1, 2, 3)	1✔
56	msg = MagneticSpaceGroup("Fm-3m")	1✔
57	assert msg.is_compatible(cubic)	1✔
58	assert not msg.is_compatible(hexagonal)	1✔
59	msg = MagneticSpaceGroup("Pnma")	1✔
60	assert msg.is_compatible(cubic)	1✔
61	assert msg.is_compatible(tet)	1✔
62	assert msg.is_compatible(ortho)	1✔
63	assert not msg.is_compatible(rhom)	1✔
64	assert not msg.is_compatible(hexagonal)	1✔
65	msg = MagneticSpaceGroup("P2/c")	1✔
66	assert msg.is_compatible(cubic)	1✔
67	assert msg.is_compatible(tet)	1✔
68	assert msg.is_compatible(ortho)	1✔
69	assert not msg.is_compatible(rhom)	1✔
70	assert not msg.is_compatible(hexagonal)	1✔
71	msg = MagneticSpaceGroup("P-1")	1✔
72	assert msg.is_compatible(cubic)	1✔
73	assert msg.is_compatible(tet)	1✔
74	assert msg.is_compatible(ortho)	1✔
75	assert msg.is_compatible(rhom)	1✔
76	assert msg.is_compatible(hexagonal)	1✔
77
78	def test_symmetry_ops(self):	1✔
79	msg_1_symmops = "\n".join(map(str, self.msg_1.symmetry_ops))	1✔
80	msg_1_symmops_ref = """x, y, z, +1	1✔
81	-x+3/4, -y+3/4, z, +1
82	-x, -y, -z, +1
83	x+1/4, y+1/4, -z, +1
84	x, -y+3/4, -z+3/4, -1
85	-x+3/4, y, -z+3/4, -1
86	-x, y+1/4, z+1/4, -1
87	x+1/4, -y, z+1/4, -1
88	x, y+1/2, z+1/2, +1
89	-x+3/4, -y+5/4, z+1/2, +1
90	-x, -y+1/2, -z+1/2, +1
91	x+1/4, y+3/4, -z+1/2, +1
92	x, -y+5/4, -z+5/4, -1
93	-x+3/4, y+1/2, -z+5/4, -1
94	-x, y+3/4, z+3/4, -1
95	x+1/4, -y+1/2, z+3/4, -1
96	x+1/2, y, z+1/2, +1
97	-x+5/4, -y+3/4, z+1/2, +1
98	-x+1/2, -y, -z+1/2, +1
99	x+3/4, y+1/4, -z+1/2, +1
100	x+1/2, -y+3/4, -z+5/4, -1
101	-x+5/4, y, -z+5/4, -1
102	-x+1/2, y+1/4, z+3/4, -1
103	x+3/4, -y, z+3/4, -1
104	x+1/2, y+1/2, z, +1
105	-x+5/4, -y+5/4, z, +1
106	-x+1/2, -y+1/2, -z, +1
107	x+3/4, y+3/4, -z, +1
108	x+1/2, -y+5/4, -z+3/4, -1
109	-x+5/4, y+1/2, -z+3/4, -1
110	-x+1/2, y+3/4, z+1/4, -1
111	x+3/4, -y+1/2, z+1/4, -1"""
112	self.assertStrContentEqual(msg_1_symmops, msg_1_symmops_ref)	1✔
113
114	msg_2_symmops = "\n".join(map(str, self.msg_2.symmetry_ops))	1✔
115	msg_2_symmops_ref = """x, y, z, +1	1✔
116	-x, y+1/2, -z, +1
117	-x, -y, -z, +1
118	x, -y+1/2, z, +1
119	x+1/2, -y+1/2, -z+1/2, -1
120	-x+1/2, -y, z+1/2, -1
121	-x+1/2, y+1/2, z+1/2, -1
122	x+1/2, y, -z+1/2, -1"""
123	self.assertStrContentEqual(msg_2_symmops, msg_2_symmops_ref)	1✔
124
125	msg_3_symmops = "\n".join(map(str, self.msg_3.symmetry_ops))	1✔
126	msg_3_symmops_ref = """x, y, z, +1	1✔
127	x, -y, -z, +1
128	-x, y, -z+1/2, +1
129	-x, -y, z+1/2, +1
130	x, y+1/2, z+1/2, -1
131	x+1/2, -y, -z+1/2, -1
132	-x+1/2, y, -z, -1
133	-x+1/2, -y, z, -1
134	x+1/2, y+1/2, z, +1
135	x+1/2, -y+1/2, -z, +1
136	-x+1/2, y+1/2, -z+1/2, +1
137	-x+1/2, -y+1/2, z+1/2, +1
138	x+1/2, y, z+1/2, -1
139	x, -y+1/2, -z+1/2, -1
140	-x, y+1/2, -z, -1
141	-x, -y+1/2, z, -1"""
142	assert msg_3_symmops == msg_3_symmops_ref	1✔
143
144	msg_4_symmops = "\n".join(map(str, self.msg_4.symmetry_ops))	1✔
145	msg_4_symmops_ref = """x, y, z, +1	1✔
146	-x, -y, -z, +1
147	x+1/2, y, z, -1
148	-x+1/2, -y, -z, -1"""
149	assert msg_4_symmops == msg_4_symmops_ref	1✔
150
151	def test_equivalence_to_spacegroup(self):	1✔
152	# first 230 magnetic space groups have same symmetry operations
153	# as normal space groups, so should give same orbits
154
155	labels = ["Fm-3m", "Pnma", "P2/c", "P-1"]	1✔
156
157	points = [[0, 0, 0], [0.5, 0, 0], [0.11, 0.22, 0.33]]	1✔
158
159	for label in labels:	1✔
160	sg = SpaceGroup(label)	1✔
161	msg = MagneticSpaceGroup(label)	1✔
162	assert sg.crystal_system == msg.crystal_system	1✔
163	for p in points:	1✔
164	pp_sg = np.array(sg.get_orbit(p))	1✔
165	pp_msg = np.array(msg.get_orbit(p, 0)[0]) # discarding magnetic moment information	1✔
166	pp_sg = pp_sg[np.lexsort(np.transpose(pp_sg)[::-1])] # sorting arrays so we can compare them	1✔
167	pp_msg = pp_msg[np.lexsort(np.transpose(pp_msg)[::-1])]	1✔
168	assert np.allclose(pp_sg, pp_msg)	1✔
169
170	def test_str(self):	1✔
171	msg = MagneticSpaceGroup([4, 11])	1✔
172
173	ref_string = """BNS: 4.11 P_b2_1	1✔
174	Operators: (1\|0,0,0) (2y\|0,1/2,0) (1\|0,1/2,0)' (2y\|0,0,0)'
175	Wyckoff Positions:
176	4e (x,y,z;mx,my,mz) (-x,y+1/2,-z;-mx,my,-mz) (x,y+1/2,z;-mx,-my,-mz)
177	(-x,y,-z;mx,-my,mz)
178	2d (1/2,y,1/2;mx,0,mz) (1/2,y+1/2,1/2;-mx,0,-mz)
179	2c (1/2,y,0;mx,0,mz) (1/2,y+1/2,0;-mx,0,-mz)
180	2b (0,y,1/2;mx,0,mz) (0,y+1/2,1/2;-mx,0,-mz)
181	2a (0,y,0;mx,0,mz) (0,y+1/2,0;-mx,0,-mz)
182	Alternative OG setting exists for this space group."""
183
184	ref_string_all = """BNS: 4.11 P_b2_1 OG: 3.7.14 P_2b2'	1✔
185	OG-BNS Transform: (a,2b,c;0,0,0)
186	Operators (BNS): (1\|0,0,0) (2y\|0,1/2,0) (1\|0,1/2,0)' (2y\|0,0,0)'
187	Wyckoff Positions (BNS):
188	4e (x,y,z;mx,my,mz) (-x,y+1/2,-z;-mx,my,-mz) (x,y+1/2,z;-mx,-my,-mz)
189	(-x,y,-z;mx,-my,mz)
190	2d (1/2,y,1/2;mx,0,mz) (1/2,y+1/2,1/2;-mx,0,-mz)
191	2c (1/2,y,0;mx,0,mz) (1/2,y+1/2,0;-mx,0,-mz)
192	2b (0,y,1/2;mx,0,mz) (0,y+1/2,1/2;-mx,0,-mz)
193	2a (0,y,0;mx,0,mz) (0,y+1/2,0;-mx,0,-mz)
194	Operators (OG): (1\|0,0,0) (2y\|0,1,0) (1\|0,1,0)' (2y\|0,0,0)'
195	Wyckoff Positions (OG): (1,0,0)+ (0,2,0)+ (0,0,1)+
196	4e (x,y,z;mx,my,mz) (-x,y+1,-z;-mx,my,-mz) (x,y+1,z;-mx,-my,-mz)
197	(-x,y,-z;mx,-my,mz)
198	2d (1/2,y,1/2;mx,0,mz) (-1/2,y+1,-1/2;-mx,0,-mz)
199	2c (1/2,y,0;mx,0,mz) (-1/2,y+1,0;-mx,0,-mz)
200	2b (0,y,1/2;mx,0,mz) (0,y+1,-1/2;-mx,0,-mz)
201	2a (0,y,0;mx,0,mz) (0,y+1,0;-mx,0,-mz)"""
202
203	self.assertStrContentEqual(str(msg), ref_string)	1✔
204	self.assertStrContentEqual(msg.data_str(), ref_string_all)	1✔
205
206
207	if __name__ == "__main__":	1✔
208	unittest.main()	×

materialsproject / pymatgen / 4075885785

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