def make_supercell(args):
if args.matrix:
matrix = sanitize_matrix(args.matrix)
maker = SupercellMaker(args.unitcell, matrix)
else:
kwargs = {}
if args.min_num_atoms:
kwargs["min_num_atoms"] = args.min_num_atoms
if args.max_num_atoms:
kwargs["max_num_atoms"] = args.max_num_atoms
maker = SupercellMaker(args.unitcell, **kwargs)
maker.supercell.structure.to(filename="SPOSCAR")
maker.supercell_info.to_json_file()
def test_create_supercell_tetragonal(tetra_close_to_cubic):
cs = SupercellMaker(tetra_close_to_cubic)
actual = cs.supercell.matrix
expected =[[ 5, 5, 0],
[-5, 5, 0],
[ 0, 0, 5]]
np.testing.assert_array_equal(actual, expected)
def test_spglib_cyclic_behavior():
structure = Structure.from_str("""Ca4 Sc2 Sb2 O12
1.0
5.469740 0.000000 0.000000
0.000000 5.632621 0.000000
-5.471566 0.000000 7.830251
O
12
direct
0.242539 0.802107 0.449144
0.242539 0.697893 0.949144
0.757461 0.197893 0.550856
0.757461 0.302107 0.050856
0.859254 0.791326 0.05328
0.859254 0.708674 0.55328
0.140746 0.208674 0.94672
0.140746 0.291326 0.44672
0.656928 0.965329 0.256023
0.656928 0.534671 0.756023
0.343072 0.034671 0.743977
0.343072 0.465329 0.243977
""", fmt="POSCAR")
sm = SupercellMaker(structure)
assert sm.conv_structure == structure
def test_transformation_matrix():
structure = Structure.from_str("""
1.0
-2.5007160000000002 2.5007160000000002 3.6755999999999993
2.5007160000000002 -2.5007159999999988 3.6755999999999993
2.5007160000000002 2.5007159999999988 -3.6755999999999993
Si
2
Direct
0.7500000000000001 0.2500000000000001 0.5000000000000000
0.0000000000000000 0.0000000000000000 0.0000000000000000""", fmt="POSCAR")
conv_structure = Structure.from_str("""
1.0
5.001432 0.000000 0.000000
0.000000 5.001432 0.000000
0.000000 0.000000 7.351200
Si
4
direct
0.000000 0.500000 0.250000 Si
0.500000 1.000000 0.750000 Si
0.000000 0.000000 0.000000 Si
0.500000 0.500000 0.500000 Si""", fmt="POSCAR")
matrix_to_conv_cell = [[3, 0, 0], [0, 3, 0], [0, 0, 2]]
sm = SupercellMaker(structure,
matrix_to_conv_cell=matrix_to_conv_cell,
symprec=0.01)
actual = structure * sm.transformation_matrix
expected = conv_structure * matrix_to_conv_cell
assert actual == expected
def test_create_supercell_generate_supercell_info(simple_cubic):
cs = SupercellMaker(simple_cubic, matrix_to_conv_cell=[[2, 0, 0], [0, 2, 0], [0, 0, 2]])
info = cs.supercell_info
assert info.transformation_matrix == [[2, 0, 0], [0, 2, 0], [0, 0, 2]]
assert info.sites["H1"].wyckoff_letter == "a"
assert info.sites["H1"].equivalent_atoms == list(range(8))
assert info.unitcell_structure == simple_cubic
def test_create_supercell_matrix(a_centered_orthorhombic):
matrix = [[2, 0, 0], [0, 1, 0], [0, 0, 1]]
cs = SupercellMaker(a_centered_orthorhombic, matrix_to_conv_cell=matrix)
actual = cs.supercell.matrix
np.testing.assert_array_equal(actual, matrix)
expected = [[2, 0, 0], [0, 1, -1], [0, 1, 1]]
np.testing.assert_array_equal(cs.transformation_matrix, expected)
def test_create_supercell(a_centered_orthorhombic):
cs = SupercellMaker(a_centered_orthorhombic)
actual_lattice = cs.conv_structure.lattice
expected = Lattice.orthorhombic(1, 4, 6)
assert actual_lattice == expected
actual = cs.supercell.matrix
expected = [[6, 0, 0], [0, 2, 0], [0, 0, 1]]
np.testing.assert_array_equal(actual, expected)
def test_rhombohedral_supercell_info():
"""There is a bug in spglib to find the inequivalent sites in supercell"""
structure = Structure.from_str(""" Ba4 Nb2 W1 O12
1.00000000000000
2.8901645462281422 1.6686372788168120 9.3650384663595574
-2.8901645462281422 1.6686372788168120 9.3650384663595574
0.0000000000000000 -3.3372745575340472 9.3650384663596231
Ba Nb W O
4 2 1 12
Direct
0.2900069010571258 0.2900069010571258 0.2900069010571258
0.7114602455184809 0.7114602455184809 0.7114602455184809
0.1345447049748643 0.1345447049748643 0.1345447049748643
0.8646114100059918 0.8646114100059918 0.8646114100059918
0.0006723681882974 0.0006723681882974 0.0006723681882974
0.4240665571167241 0.4240665571167241 0.4240665571167241
0.5787478829344508 0.5787478829344508 0.5787478829344508
0.7884796629179860 0.2974972818896759 0.7884796629179860
0.2974972818896759 0.7884796629179860 0.7884796629179860
0.7884796629179860 0.7884796629179860 0.2974972818896759
0.2034890710071906 0.7099376271089710 0.2034890710071906
0.7099376271089710 0.2034890710071906 0.2034890710071906
0.2034890710071906 0.2034890710071906 0.7099376271089710
0.6204119903421983 0.1229791605843715 0.6204119903421983
0.1229791605843715 0.6204119903421983 0.6204119903421983
0.6204119903421983 0.6204119903421983 0.1229791605843715
0.3875918889522652 0.8655326340817453 0.3875918889522652
0.8655326340817453 0.3875918889522652 0.3875918889522652
0.3875918889522652 0.3875918889522652 0.8655326340817453""",
fmt="poscar")
sm = SupercellMaker(structure,
symprec=0.01,
min_num_atoms=60,
max_num_atoms=500)
assert "O5" not in sm.supercell_info.sites.keys()
def test_create_supercell_raise_not_primitive_error(bcc):
with pytest.raises(NotPrimitiveError):
SupercellMaker(primitive_structure=bcc)