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Use refined structure when using CifWriter with symprec. Fixes #241.
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@shyuep
shyuep committed Oct 2, 2015
1 parent ccfa968 commit 17b7011
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Showing 2 changed files with 263 additions and 33 deletions.
10 changes: 7 additions & 3 deletions pymatgen/io/cif.py
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Original file line number Diff line number Diff line change
Expand Up @@ -588,14 +588,18 @@ def __init__(self, struct, symprec=None):

block = OrderedDict()
loops = []
latt = struct.lattice
comp = struct.composition
no_oxi_comp = comp.element_composition
spacegroup = ("P 1", 1)
if symprec is not None:
sf = SpacegroupAnalyzer(struct, symprec)
spacegroup = (sf.get_spacegroup_symbol(),
sf.get_spacegroup_number())
# Needs the refined struture when using symprec. This converts
# primitive to conventional structures, the standard for CIF.
struct = sf.get_refined_structure()

latt = struct.lattice
comp = struct.composition
no_oxi_comp = comp.element_composition
block["_symmetry_space_group_name_H-M"] = spacegroup[0]
for cell_attr in ['a', 'b', 'c']:
block["_cell_length_" + cell_attr] = format_str.format(
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286 changes: 256 additions & 30 deletions pymatgen/io/tests/test_cif.py
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Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@
from pymatgen.io.vasp.inputs import Poscar
from pymatgen import Element, Specie, Lattice, Structure, Composition, DummySpecie
from pymatgen.analysis.structure_matcher import StructureMatcher

from pymatgen.util.testing import PymatgenTest

test_dir = os.path.join(os.path.dirname(__file__), "..", "..", "..",
'test_files')
Expand Down Expand Up @@ -159,7 +159,7 @@ def test_long_loop(self):
self.assertEqual(str(CifBlock(data, loops, 'test')), cif_str)


class CifIOTest(unittest.TestCase):
class CifIOTest(PymatgenTest):

def test_CifParser(self):
parser = CifParser(os.path.join(test_dir, 'LiFePO4.cif'))
Expand Down Expand Up @@ -313,13 +313,11 @@ def test_CifWriter(self):
_atom_site_fract_y
_atom_site_fract_z
_atom_site_occupancy
Fe Fe1 4 0.218728 0.750000 0.474867 1
P P2 4 0.094613 0.250000 0.418243 1
O O3 8 0.165710 0.046072 0.285384 1
O O4 4 0.043372 0.750000 0.707138 1
O O5 4 0.096642 0.250000 0.741320 1
"""
Fe Fe1 4 0.218728 0.250000 0.525133 1
P P2 4 0.094613 0.750000 0.581757 1
O O3 8 0.165710 0.546072 0.714616 1
O O4 4 0.043372 0.250000 0.292862 1
O O5 4 0.096642 0.750000 0.258680 1"""
for l1, l2 in zip(str(writer).split("\n"), ans.split("\n")):
self.assertEqual(l1.strip(), l2.strip())

Expand Down Expand Up @@ -360,37 +358,37 @@ def test_symmetrized(self):
_atom_site_fract_y
_atom_site_fract_z
_atom_site_occupancy
Fe Fe1 4 0.218728 0.750000 0.474867 1
P P2 4 0.094613 0.250000 0.418243 1
O O3 8 0.165710 0.046072 0.285384 1
O O4 4 0.043372 0.750000 0.707138 1
O O5 4 0.096642 0.250000 0.741320 1"""
Fe Fe1 4 0.218728 0.250000 0.525133 1
P P2 4 0.094613 0.750000 0.581757 1
O O3 8 0.165710 0.546072 0.714616 1
O O4 4 0.043372 0.250000 0.292862 1
O O5 4 0.096642 0.750000 0.258680 1"""
for l1, l2 in zip(str(writer).split("\n"), ans.split("\n")):
self.assertEqual(l1.strip(), l2.strip())

ans = """# generated using pymatgen
data_LiFePO4
_symmetry_space_group_name_H-M Pnma
_cell_length_a 4.74480000
_cell_length_a 10.41037000
_cell_length_b 6.06577000
_cell_length_c 10.41037000
_cell_angle_alpha 90.50179000
_cell_angle_beta 90.00019000
_cell_angle_gamma 90.00362000
_cell_length_c 4.74480000
_cell_angle_alpha 90.00000000
_cell_angle_beta 90.00000000
_cell_angle_gamma 90.00000000
_symmetry_Int_Tables_number 62
_chemical_formula_structural LiFePO4
_chemical_formula_sum 'Li4 Fe4 P4 O16'
_cell_volume 299.607967711
_cell_volume 299.619458734
_cell_formula_units_Z 4
loop_
_symmetry_equiv_pos_site_id
_symmetry_equiv_pos_as_xyz
1 'x, y, z'
2 '-x, -y, -z'
3 'x+1/2, -y, -z+1/2'
4 '-x+1/2, y, z+1/2'
5 '-x+1/2, -y+1/2, z+1/2'
6 'x+1/2, y+1/2, -z+1/2'
3 '-x+1/2, -y, z+1/2'
4 'x+1/2, y, -z+1/2'
5 'x+1/2, -y+1/2, -z+1/2'
6 '-x+1/2, y+1/2, z+1/2'
7 '-x, y+1/2, -z'
8 'x, -y+1/2, z'
loop_
Expand All @@ -401,17 +399,245 @@ def test_symmetrized(self):
_atom_site_fract_y
_atom_site_fract_z
_atom_site_occupancy
Li Li1 4 0.000010 0.500000 0.999990 1.0
Fe Fe2 4 0.025030 0.746540 0.281160 1.0
P P3 4 0.082060 0.248260 0.405570 1.0
O O4 8 0.213420 0.043980 0.334230 1.0
O O5 4 0.208430 0.251100 0.543180 1.0
O O6 4 0.241480 0.750450 0.596220 1.0
Li Li1 4 0.000000 0.000000 0.000000 1.0
Fe Fe2 4 0.218845 0.750000 0.474910 1.0
P P3 4 0.094445 0.250000 0.417920 1.0
O O4 8 0.165815 0.044060 0.286540 1.0
O O5 4 0.043155 0.750000 0.708460 1.0
O O6 4 0.096215 0.250000 0.741480 1.0
"""
s = Structure.from_file(os.path.join(test_dir, 'LiFePO4.cif'))
writer = CifWriter(s, symprec=0.1)
self.assertEqual(writer.__str__().strip(), ans.strip())

s = self.get_structure("Li2O")
writer = CifWriter(s, symprec=0.1)
ans = """# generated using pymatgen
data_Li2O
_symmetry_space_group_name_H-M Fm-3m
_cell_length_a 4.61000000
_cell_length_b 4.61000000
_cell_length_c 4.61000000
_cell_angle_alpha 90.00000000
_cell_angle_beta 90.00000000
_cell_angle_gamma 90.00000000
_symmetry_Int_Tables_number 225
_chemical_formula_structural Li2O
_chemical_formula_sum 'Li8 O4'
_cell_volume 97.972181
_cell_formula_units_Z 4
loop_
_symmetry_equiv_pos_site_id
_symmetry_equiv_pos_as_xyz
1 'x, y, z'
2 '-x, -y, -z'
3 'z, y, -x'
4 '-z, -y, x'
5 '-x, y, -z'
6 'x, -y, z'
7 '-z, y, x'
8 'z, -y, -x'
9 'x, -y, -z'
10 '-x, y, z'
11 'z, -y, x'
12 '-z, y, -x'
13 '-x, -y, z'
14 'x, y, -z'
15 '-z, -y, -x'
16 'z, y, x'
17 'y, -z, -x'
18 '-y, z, x'
19 'y, x, -z'
20 '-y, -x, z'
21 'y, z, x'
22 '-y, -z, -x'
23 'y, -x, z'
24 '-y, x, -z'
25 '-y, z, -x'
26 'y, -z, x'
27 '-y, -x, -z'
28 'y, x, z'
29 '-y, -z, x'
30 'y, z, -x'
31 '-y, x, z'
32 'y, -x, -z'
33 '-z, x, -y'
34 'z, -x, y'
35 'x, z, -y'
36 '-x, -z, y'
37 'z, -x, -y'
38 '-z, x, y'
39 '-x, -z, -y'
40 'x, z, y'
41 'z, x, y'
42 '-z, -x, -y'
43 '-x, z, y'
44 'x, -z, -y'
45 '-z, -x, y'
46 'z, x, -y'
47 'x, -z, y'
48 '-x, z, -y'
49 'x+1/2, y+1/2, z'
50 '-x+1/2, -y+1/2, -z'
51 'z+1/2, y+1/2, -x'
52 '-z+1/2, -y+1/2, x'
53 '-x+1/2, y+1/2, -z'
54 'x+1/2, -y+1/2, z'
55 '-z+1/2, y+1/2, x'
56 'z+1/2, -y+1/2, -x'
57 'x+1/2, -y+1/2, -z'
58 '-x+1/2, y+1/2, z'
59 'z+1/2, -y+1/2, x'
60 '-z+1/2, y+1/2, -x'
61 '-x+1/2, -y+1/2, z'
62 'x+1/2, y+1/2, -z'
63 '-z+1/2, -y+1/2, -x'
64 'z+1/2, y+1/2, x'
65 'y+1/2, -z+1/2, -x'
66 '-y+1/2, z+1/2, x'
67 'y+1/2, x+1/2, -z'
68 '-y+1/2, -x+1/2, z'
69 'y+1/2, z+1/2, x'
70 '-y+1/2, -z+1/2, -x'
71 'y+1/2, -x+1/2, z'
72 '-y+1/2, x+1/2, -z'
73 '-y+1/2, z+1/2, -x'
74 'y+1/2, -z+1/2, x'
75 '-y+1/2, -x+1/2, -z'
76 'y+1/2, x+1/2, z'
77 '-y+1/2, -z+1/2, x'
78 'y+1/2, z+1/2, -x'
79 '-y+1/2, x+1/2, z'
80 'y+1/2, -x+1/2, -z'
81 '-z+1/2, x+1/2, -y'
82 'z+1/2, -x+1/2, y'
83 'x+1/2, z+1/2, -y'
84 '-x+1/2, -z+1/2, y'
85 'z+1/2, -x+1/2, -y'
86 '-z+1/2, x+1/2, y'
87 '-x+1/2, -z+1/2, -y'
88 'x+1/2, z+1/2, y'
89 'z+1/2, x+1/2, y'
90 '-z+1/2, -x+1/2, -y'
91 '-x+1/2, z+1/2, y'
92 'x+1/2, -z+1/2, -y'
93 '-z+1/2, -x+1/2, y'
94 'z+1/2, x+1/2, -y'
95 'x+1/2, -z+1/2, y'
96 '-x+1/2, z+1/2, -y'
97 'x+1/2, y, z+1/2'
98 '-x+1/2, -y, -z+1/2'
99 'z+1/2, y, -x+1/2'
100 '-z+1/2, -y, x+1/2'
101 '-x+1/2, y, -z+1/2'
102 'x+1/2, -y, z+1/2'
103 '-z+1/2, y, x+1/2'
104 'z+1/2, -y, -x+1/2'
105 'x+1/2, -y, -z+1/2'
106 '-x+1/2, y, z+1/2'
107 'z+1/2, -y, x+1/2'
108 '-z+1/2, y, -x+1/2'
109 '-x+1/2, -y, z+1/2'
110 'x+1/2, y, -z+1/2'
111 '-z+1/2, -y, -x+1/2'
112 'z+1/2, y, x+1/2'
113 'y+1/2, -z, -x+1/2'
114 '-y+1/2, z, x+1/2'
115 'y+1/2, x, -z+1/2'
116 '-y+1/2, -x, z+1/2'
117 'y+1/2, z, x+1/2'
118 '-y+1/2, -z, -x+1/2'
119 'y+1/2, -x, z+1/2'
120 '-y+1/2, x, -z+1/2'
121 '-y+1/2, z, -x+1/2'
122 'y+1/2, -z, x+1/2'
123 '-y+1/2, -x, -z+1/2'
124 'y+1/2, x, z+1/2'
125 '-y+1/2, -z, x+1/2'
126 'y+1/2, z, -x+1/2'
127 '-y+1/2, x, z+1/2'
128 'y+1/2, -x, -z+1/2'
129 '-z+1/2, x, -y+1/2'
130 'z+1/2, -x, y+1/2'
131 'x+1/2, z, -y+1/2'
132 '-x+1/2, -z, y+1/2'
133 'z+1/2, -x, -y+1/2'
134 '-z+1/2, x, y+1/2'
135 '-x+1/2, -z, -y+1/2'
136 'x+1/2, z, y+1/2'
137 'z+1/2, x, y+1/2'
138 '-z+1/2, -x, -y+1/2'
139 '-x+1/2, z, y+1/2'
140 'x+1/2, -z, -y+1/2'
141 '-z+1/2, -x, y+1/2'
142 'z+1/2, x, -y+1/2'
143 'x+1/2, -z, y+1/2'
144 '-x+1/2, z, -y+1/2'
145 'x, y+1/2, z+1/2'
146 '-x, -y+1/2, -z+1/2'
147 'z, y+1/2, -x+1/2'
148 '-z, -y+1/2, x+1/2'
149 '-x, y+1/2, -z+1/2'
150 'x, -y+1/2, z+1/2'
151 '-z, y+1/2, x+1/2'
152 'z, -y+1/2, -x+1/2'
153 'x, -y+1/2, -z+1/2'
154 '-x, y+1/2, z+1/2'
155 'z, -y+1/2, x+1/2'
156 '-z, y+1/2, -x+1/2'
157 '-x, -y+1/2, z+1/2'
158 'x, y+1/2, -z+1/2'
159 '-z, -y+1/2, -x+1/2'
160 'z, y+1/2, x+1/2'
161 'y, -z+1/2, -x+1/2'
162 '-y, z+1/2, x+1/2'
163 'y, x+1/2, -z+1/2'
164 '-y, -x+1/2, z+1/2'
165 'y, z+1/2, x+1/2'
166 '-y, -z+1/2, -x+1/2'
167 'y, -x+1/2, z+1/2'
168 '-y, x+1/2, -z+1/2'
169 '-y, z+1/2, -x+1/2'
170 'y, -z+1/2, x+1/2'
171 '-y, -x+1/2, -z+1/2'
172 'y, x+1/2, z+1/2'
173 '-y, -z+1/2, x+1/2'
174 'y, z+1/2, -x+1/2'
175 '-y, x+1/2, z+1/2'
176 'y, -x+1/2, -z+1/2'
177 '-z, x+1/2, -y+1/2'
178 'z, -x+1/2, y+1/2'
179 'x, z+1/2, -y+1/2'
180 '-x, -z+1/2, y+1/2'
181 'z, -x+1/2, -y+1/2'
182 '-z, x+1/2, y+1/2'
183 '-x, -z+1/2, -y+1/2'
184 'x, z+1/2, y+1/2'
185 'z, x+1/2, y+1/2'
186 '-z, -x+1/2, -y+1/2'
187 '-x, z+1/2, y+1/2'
188 'x, -z+1/2, -y+1/2'
189 '-z, -x+1/2, y+1/2'
190 'z, x+1/2, -y+1/2'
191 'x, -z+1/2, y+1/2'
192 '-x, z+1/2, -y+1/2'
loop_
_atom_type_symbol
_atom_type_oxidation_number
Li+ 1.0
O2- -2.0
loop_
_atom_site_type_symbol
_atom_site_label
_atom_site_symmetry_multiplicity
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_occupancy
Li+ Li1 8 0.250000 0.250000 0.250000 1.0
O2- O2 4 0.000000 0.000000 0.000000 1.0"""
self.assertEqual(writer.__str__().strip(), ans.strip())

def test_disordered(self):
si = Element("Si")
n = Element("N")
Expand Down

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