def test_symmetrize_defect_structure_wo_anchor():
structure = Structure.from_str(fmt="poscar",
input_string="""Mg4 O3
1.00000000000000
5 0 0
0 5 0
0 0 5
Mg O
4 3
Direct
0.01 0.01 0.01
0.01 0.51 0.51
0.51 0.01 0.51
0.51 0.51 0.01
0.51 0.51 0.51
0.01 0.01 0.51
0.01 0.51 0.01""")
actual = refine_defect_structure(structure=structure)
assert actual is None
def test_symmetrize_defect_structure(before_refine, after_refine):
actual = refine_defect_structure(before_refine,
anchor_atom_index=1,
anchor_atom_coords=np.array(
[0.0, 0.5, 0.5]))
assert actual == after_refine
def test_symmetrize_defect_structure_2():
structure = Structure.from_str(fmt="poscar",
input_string="""Mg48 N31
1.00000000000000
10.00 0.00 0.00
0.00 10.00 0.00
0.00 0.00 10.00
N
31
Direct
0.9998735951099533 0.9999339271342436 0.9998810782738516
0.4998325344890802 0.0000864604371742 0.0001093145892668
0.9999579188430090 0.5001853666498661 0.0001277381372233
0.2491639910909313 0.2182663238872422 0.4987861655656971
0.2808293379596023 0.4991743721150215 0.7498359204125151
0.5007987323114946 0.2498921962049820 0.2191539974347521
0.2186260754052398 0.4998463318536253 0.2504951842089369
0.5003683092799207 0.7505911171114192 0.2814698995089699
0.7491029691281099 0.2824156531954642 0.4998653178588484
0.2496769296641759 0.2810133141130393 0.0008972384265746
0.2179934993920654 0.0013328906653882 0.7491830895564036
0.9985995146190305 0.2494223137356002 0.2817274775328684
0.2819549960242611 0.0002510594995684 0.2492863143591961
0.9999066837513126 0.7494408251560003 0.2182162389686653
0.7503446162775589 0.2186089947761758 0.0001821657373426
0.5000178504783079 0.5000386610406409 0.9999895875233165
0.4999380720704565 0.5002342427150381 0.5000689317878368
0.0000976472392296 0.5000243131273407 0.5000777225283457
0.5001616481443207 0.0002089601314523 0.4998675396277079
0.7502599885437249 0.7191435719333086 0.9992528941462950
0.7820064323950149 0.9990033992670391 0.2509026823008185
0.0012722293791043 0.7506950871201497 0.7182763220765622
0.7176368346430237 0.9998582962107960 0.7509680009789932
0.0000228430868177 0.2509182464808006 0.7821761073165092
0.2495215811710665 0.7814963684974714 0.9998566240987685
0.7508300518084354 0.7818602560717594 0.5013867902350881
0.7190618878688895 0.5010405127949369 0.2502514755283229
0.4989978969018409 0.7502977850544852 0.7809492219327865
0.7814464623477875 0.5003886730650109 0.7494947707104060
0.4996606931909255 0.2496508616713697 0.7186036919929819
0.2506716727065808 0.7181216545822622 0.5001902272634595""")
actual = refine_defect_structure(structure,
anchor_atom_index=15,
anchor_atom_coords=np.array(
[0.5, 0.5, 0.0]))
expected = Structure.from_str(fmt="poscar",
input_string="""Mg4 O3
1.00000000000000
10 0 0
0 10 0
0 0 10
N
31
Direct
0 0 0
0.5 0 0
0 0.5 0
0.249164 0.218235 0.498835
0.280829 0.499143 0.749885
0.500857 0.249885 0.219171
0.218626 0.499815 0.250544
0.500185 0.750544 0.281374
0.749103 0.282384 0.499914
0.249885 0.280829 0.000857
0.218235 0.001165 0.749164
0.998835 0.249164 0.281765
0.282384 8.6e-05 0.249103
0.999914 0.749103 0.217616
0.750544 0.218626 0.000185
0.5 0.5 0
0.5 0.5 0.5
0 0.5 0.5
0.5 1 0.5
0.750115 0.719171 0.999143
0.781765 0.998835 0.250836
0.001165 0.750836 0.718235
0.717616 0.999914 0.750897
8.6e-05 0.250897 0.782384
0.249456 0.781374 0.999815
0.750836 0.781765 0.501165
0.719171 0.500857 0.250115
0.499143 0.750115 0.780829
0.781374 0.500185 0.749456
0.499815 0.249456 0.718626
0.250897 0.717616 0.500086""")
assert actual == expected
def make_refine_defect_poscar(args):
structure = refine_defect_structure(args.structure,
args.defect_entry.anchor_atom_index,
args.defect_entry.anchor_atom_coords)
if structure:
print(structure.to(fmt="poscar", filename=args.poscar_name))