def test_fold_coords():
actual = Structure(Lattice.monoclinic(a=1, b=1, c=1, beta=20),
species=["H"],
coords=[[0.5, 0, 0.49]])
fold_coords_in_structure(actual, [0, 0, 0])
expected = Structure(Lattice.monoclinic(a=1, b=1, c=1, beta=20),
species=["H"],
coords=[[-0.5, 0, 0.49]])
assert actual == expected
def test_sulfide_type(self):
# NaS2 -> polysulfide
latt = Lattice.tetragonal(9.59650, 11.78850)
species = ["Na"] * 2 + ["S"] * 2
coords = [[0.00000, 0.00000, 0.17000], [0.27600, 0.25000, 0.12500],
[0.03400, 0.25000, 0.29600], [0.14700, 0.11600, 0.40000]]
struct = Structure.from_spacegroup(122, latt, species, coords)
self.assertEqual(sulfide_type(struct), "polysulfide")
# NaCl type NaS -> sulfide
latt = Lattice.cubic(5.75)
species = ["Na", "S"]
coords = [[0.00000, 0.00000, 0.00000], [0.50000, 0.50000, 0.50000]]
struct = Structure.from_spacegroup(225, latt, species, coords)
self.assertEqual(sulfide_type(struct), "sulfide")
# Na2S2O3 -> None (sulfate)
latt = Lattice.monoclinic(6.40100, 8.10000, 8.47400, 96.8800)
species = ["Na"] * 2 + ["S"] * 2 + ["O"] * 3
coords = [[0.29706, 0.62396, 0.08575], [0.37673, 0.30411, 0.45416],
[0.52324, 0.10651, 0.21126], [0.29660, -0.04671, 0.26607],
[0.17577, 0.03720, 0.38049], [0.38604, -0.20144, 0.33624],
[0.16248, -0.08546, 0.11608]]
struct = Structure.from_spacegroup(14, latt, species, coords)
self.assertEqual(sulfide_type(struct), None)
# Na3PS3O -> sulfide
latt = Lattice.orthorhombic(9.51050, 11.54630, 5.93230)
species = ["Na"] * 2 + ["S"] * 2 + ["P", "O"]
coords = [[0.19920, 0.11580, 0.24950], [0.00000, 0.36840, 0.29380],
[0.32210, 0.36730, 0.22530], [0.50000, 0.11910, 0.27210],
[0.50000, 0.29400, 0.35500], [0.50000, 0.30300, 0.61140]]
struct = Structure.from_spacegroup(36, latt, species, coords)
self.assertEqual(sulfide_type(struct), "sulfide")
def test_from_structure(self):
latt = Lattice.monoclinic(9.78746, 4.75058, 8.95892, 115.9693)
structure = Structure.from_spacegroup(
15,
latt,
["Os", "O", "O"],
[
[0, 0.25583, 0.75],
[0.11146, 0.46611, 0.91631],
[0.11445, 0.04564, 0.69518],
],
)
velocities = np.random.randn(20, 3) * 0.1
structure.add_site_property("velocities", velocities)
ld = LammpsData.from_structure(structure=structure,
ff_elements=["O", "Os", "Na"])
i = random.randint(0, 19)
a = latt.matrix[0]
va = velocities[i].dot(a) / np.linalg.norm(a)
self.assertAlmostEqual(va, ld.velocities.loc[i + 1, "vx"])
self.assertAlmostEqual(velocities[i, 1], ld.velocities.loc[i + 1,
"vy"])
np.testing.assert_array_almost_equal(ld.masses["mass"],
[22.989769, 190.23, 15.9994])
np.testing.assert_array_equal(ld.atoms["type"], [2] * 4 + [3] * 16)
def complex_monoclinic():
lattice = Lattice.monoclinic(3, 4, 5, 100)
coords = [[0.0, 0.0, 0.0], [0.1, 0.0, 0.0], [0.9, 0.0, 0.0],
[0.2, 0.0, 0.0], [0.8, 0.0, 0.0]]
return IStructure(lattice=lattice,
species=["H", "He", "He", "He", "He"],
coords=coords)
def complex_monoclinic_structure():
coords = [
[0.0, 0.0, 0.0],
[0.1, 0.0, 0.0],
[0.9, 0.0, 0.0],
[0.2, 0.0, 0.0],
[0.8, 0.0, 0.0],
]
return Structure(lattice=Lattice.monoclinic(10, 20, 30, 75),
species=["H", "He", "He", "He", "He"],
coords=coords)
def test_sulfide_type(self):
# NaS2 -> polysulfide
latt = Lattice.tetragonal(9.59650, 11.78850)
species = ["Na"] * 2 + ["S"] * 2
coords = [[0.00000, 0.00000, 0.17000],
[0.27600, 0.25000, 0.12500],
[0.03400, 0.25000, 0.29600],
[0.14700, 0.11600, 0.40000]]
struct = Structure.from_spacegroup(122, latt, species, coords)
self.assertEqual(sulfide_type(struct), "polysulfide")
# NaCl type NaS -> sulfide
latt = Lattice.cubic(5.75)
species = ["Na", "S"]
coords = [[0.00000, 0.00000, 0.00000],
[0.50000, 0.50000, 0.50000]]
struct = Structure.from_spacegroup(225, latt, species, coords)
self.assertEqual(sulfide_type(struct), "sulfide")
# Na2S2O3 -> None (sulfate)
latt = Lattice.monoclinic(6.40100, 8.10000, 8.47400, 96.8800)
species = ["Na"] * 2 + ["S"] * 2 + ["O"] * 3
coords = [[0.29706, 0.62396, 0.08575],
[0.37673, 0.30411, 0.45416],
[0.52324, 0.10651, 0.21126],
[0.29660, -0.04671, 0.26607],
[0.17577, 0.03720, 0.38049],
[0.38604, -0.20144, 0.33624],
[0.16248, -0.08546, 0.11608]]
struct = Structure.from_spacegroup(14, latt, species, coords)
self.assertEqual(sulfide_type(struct), None)
# Na3PS3O -> sulfide
latt = Lattice.orthorhombic(9.51050, 11.54630, 5.93230)
species = ["Na"] * 2 + ["S"] * 2 + ["P", "O"]
coords = [[0.19920, 0.11580, 0.24950],
[0.00000, 0.36840, 0.29380],
[0.32210, 0.36730, 0.22530],
[0.50000, 0.11910, 0.27210],
[0.50000, 0.29400, 0.35500],
[0.50000, 0.30300, 0.61140]]
struct = Structure.from_spacegroup(36, latt, species, coords)
self.assertEqual(sulfide_type(struct), "sulfide")
# test for unphysical cells
struct.scale_lattice(struct.volume*10)
self.assertEqual(sulfide_type(struct), "sulfide")
def test_from_structure(self):
latt = Lattice.monoclinic(9.78746, 4.75058, 8.95892, 115.9693)
structure = Structure.from_spacegroup(15, latt, ["Os", "O", "O"],
[[0, 0.25583, 0.75],
[0.11146, 0.46611, 0.91631],
[0.11445, 0.04564, 0.69518]])
velocities = np.random.randn(20, 3) * 0.1
structure.add_site_property("velocities", velocities)
ld = LammpsData.from_structure(structure=structure,
ff_elements=["O", "Os", "Na"])
i = random.randint(0, 19)
a = latt.matrix[0]
va = velocities[i].dot(a) / np.linalg.norm(a)
self.assertAlmostEqual(va, ld.velocities.loc[i + 1, "vx"])
self.assertAlmostEqual(velocities[i, 1],
ld.velocities.loc[i + 1, "vy"])
np.testing.assert_array_almost_equal(ld.masses["mass"],
[22.989769, 190.23, 15.9994])
np.testing.assert_array_equal(ld.atoms["type"], [2] * 4 + [3] * 16)
def c_centered_monoclinic():
lattice = Lattice.monoclinic(3, 4, 5, 100)
coords = [[0.0, 0.0, 0.0], [0.5, 0.5, 0.0]]
return IStructure(lattice=lattice, species=["H", "H"], coords=coords)
def monoclinic():
lattice = Lattice.monoclinic(3, 4, 5, 100)
coords = [[0.0, 0.0, 0.0]]
return IStructure(lattice=lattice, species=["H"], coords=coords)
