def setUp(self):
# trivial example, simple square lattice for testing
structure = Structure(Lattice.tetragonal(5.0, 50.0), ['H'], [[0, 0, 0]])
self.square_sg = StructureGraph.with_empty_graph(structure, edge_weight_name="", edge_weight_units="")
self.square_sg.add_edge(0, 0, from_jimage=(0, 0, 0), to_jimage=(1, 0, 0))
self.square_sg.add_edge(0, 0, from_jimage=(0, 0, 0), to_jimage=(-1, 0, 0))
self.square_sg.add_edge(0, 0, from_jimage=(0, 0, 0), to_jimage=(0, 1, 0))
self.square_sg.add_edge(0, 0, from_jimage=(0, 0, 0), to_jimage=(0, -1, 0))
# body-centered square lattice for testing
structure = Structure(Lattice.tetragonal(5.0, 50.0), ['H', 'He'], [[0, 0, 0], [0.5, 0.5, 0.5]])
self.bc_square_sg = StructureGraph.with_empty_graph(structure, edge_weight_name="", edge_weight_units="")
self.bc_square_sg.add_edge(0, 0, from_jimage=(0, 0, 0), to_jimage=(1, 0, 0))
self.bc_square_sg.add_edge(0, 0, from_jimage=(0, 0, 0), to_jimage=(-1, 0, 0))
self.bc_square_sg.add_edge(0, 0, from_jimage=(0, 0, 0), to_jimage=(0, 1, 0))
self.bc_square_sg.add_edge(0, 0, from_jimage=(0, 0, 0), to_jimage=(0, -1, 0))
self.bc_square_sg.add_edge(0, 1, from_jimage=(0, 0, 0), to_jimage=(0, 0, 0))
self.bc_square_sg.add_edge(0, 1, from_jimage=(0, 0, 0), to_jimage=(-1, 0, 0))
self.bc_square_sg.add_edge(0, 1, from_jimage=(0, 0, 0), to_jimage=(-1, -1, 0))
self.bc_square_sg.add_edge(0, 1, from_jimage=(0, 0, 0), to_jimage=(0, -1, 0))
# body-centered square lattice for testing
# directions reversed, should be equivalent to as bc_square
structure = Structure(Lattice.tetragonal(5.0, 50.0), ['H', 'He'], [[0, 0, 0], [0.5, 0.5, 0.5]])
self.bc_square_sg_r = StructureGraph.with_empty_graph(structure, edge_weight_name="", edge_weight_units="")
self.bc_square_sg_r.add_edge(0, 0, from_jimage=(0, 0, 0), to_jimage=(1, 0, 0))
self.bc_square_sg_r.add_edge(0, 0, from_jimage=(0, 0, 0), to_jimage=(-1, 0, 0))
self.bc_square_sg_r.add_edge(0, 0, from_jimage=(0, 0, 0), to_jimage=(0, 1, 0))
self.bc_square_sg_r.add_edge(0, 0, from_jimage=(0, 0, 0), to_jimage=(0, -1, 0))
self.bc_square_sg_r.add_edge(0, 1, from_jimage=(0, 0, 0), to_jimage=(0, 0, 0))
self.bc_square_sg_r.add_edge(1, 0, from_jimage=(-1, 0, 0), to_jimage=(0, 0, 0))
self.bc_square_sg_r.add_edge(1, 0, from_jimage=(-1, -1, 0), to_jimage=(0, 0, 0))
self.bc_square_sg_r.add_edge(1, 0, from_jimage=(0, -1, 0), to_jimage=(0, 0, 0))
# MoS2 example, structure graph obtained from critic2
# (not ground state, from mp-1023924, single layer)
stdout_file = os.path.join(os.path.dirname(__file__), "..", "..", "..",
'test_files/critic2/MoS2_critic2_stdout.txt')
with open(stdout_file, 'r') as f:
reference_stdout = f.read()
self.structure = Structure.from_file(os.path.join(os.path.dirname(__file__), "..", "..", "..",
'test_files/critic2/MoS2.cif'))
c2o = Critic2Output(self.structure, reference_stdout)
self.mos2_sg = c2o.structure_graph(edge_weight="bond_length", edge_weight_units="Å")
latt = Lattice.cubic(4.17)
species = ["Ni", "O"]
coords = [[0, 0, 0],
[0.5, 0.5, 0.5]]
self.NiO = Structure.from_spacegroup(225, latt, species, coords).get_primitive_structure()
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_lattice_2_lmpbox(self):
matrix = np.diag(np.random.randint(5, 14, size=(3,))) \
+ np.random.rand(3, 3) * 0.2 - 0.1
init_latt = Lattice(matrix)
frac_coords = np.random.rand(10, 3)
init_structure = Structure(init_latt, ["H"] * 10, frac_coords)
origin = np.random.rand(3) * 10 - 5
box, symmop = lattice_2_lmpbox(lattice=init_latt, origin=origin)
boxed_latt = box.to_lattice()
np.testing.assert_array_almost_equal(init_latt.abc, boxed_latt.abc)
np.testing.assert_array_almost_equal(init_latt.angles,
boxed_latt.angles)
cart_coords = symmop.operate_multi(init_structure.cart_coords) - origin
boxed_structure = Structure(boxed_latt, ["H"] * 10,
cart_coords,
coords_are_cartesian=True)
np.testing.assert_array_almost_equal(boxed_structure.frac_coords,
frac_coords)
tetra_latt = Lattice.tetragonal(5, 5)
tetra_box, _ = lattice_2_lmpbox(tetra_latt)
self.assertIsNone(tetra_box.tilt)
ortho_latt = Lattice.orthorhombic(5, 5, 5)
ortho_box, _ = lattice_2_lmpbox(ortho_latt)
self.assertIsNone(ortho_box.tilt)
rot_tetra_latt = Lattice([[5, 0, 0], [0, 2, 2], [0, -2, 2]])
_, rotop = lattice_2_lmpbox(rot_tetra_latt)
np.testing. \
assert_array_almost_equal(rotop.rotation_matrix,
[[1, 0, 0],
[0, 2 ** 0.5 / 2, 2 ** 0.5 / 2],
[0, -2 ** 0.5 / 2, 2 ** 0.5 / 2]])
def test_lattice_2_lmpbox(self):
matrix = np.diag(np.random.randint(5, 14, size=(3,))) \
+ np.random.rand(3, 3) * 0.2 - 0.1
init_latt = Lattice(matrix)
frac_coords = np.random.rand(10, 3)
init_structure = Structure(init_latt, ["H"] * 10, frac_coords)
origin = np.random.rand(3) * 10 - 5
box, symmop = lattice_2_lmpbox(lattice=init_latt, origin=origin)
boxed_latt = box.to_lattice()
np.testing.assert_array_almost_equal(init_latt.abc, boxed_latt.abc)
np.testing.assert_array_almost_equal(init_latt.angles,
boxed_latt.angles)
cart_coords = symmop.operate_multi(init_structure.cart_coords) \
- origin
boxed_structure = Structure(boxed_latt, ["H"] * 10, cart_coords,
coords_are_cartesian=True)
np.testing.assert_array_almost_equal(boxed_structure.frac_coords,
frac_coords)
tetra_latt = Lattice.tetragonal(5, 5)
tetra_box, _ = lattice_2_lmpbox(tetra_latt)
self.assertIsNone(tetra_box.tilt)
ortho_latt = Lattice.orthorhombic(5, 5, 5)
ortho_box, _ = lattice_2_lmpbox(ortho_latt)
self.assertIsNone(ortho_box.tilt)
rot_tetra_latt = Lattice([[5, 0, 0], [0, 2, 2], [0, -2, 2]])
_, rotop = lattice_2_lmpbox(rot_tetra_latt)
np.testing.\
assert_array_almost_equal(rotop.rotation_matrix,
[[1, 0, 0],
[0, 2 ** 0.5 / 2, 2 ** 0.5 / 2],
[0, -2 ** 0.5 / 2, 2 ** 0.5 / 2]])
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 setUp(self):
# trivial example, simple square lattice for testing
structure = Structure(Lattice.tetragonal(5.0, 50.0), ['H'],
[[0, 0, 0]])
self.square_sg = StructureGraph.with_empty_graph(structure,
edge_weight_name="",
edge_weight_units="")
self.square_sg.add_edge(0,
0,
from_jimage=(0, 0, 0),
to_jimage=(1, 0, 0))
self.square_sg.add_edge(0,
0,
from_jimage=(0, 0, 0),
to_jimage=(-1, 0, 0))
self.square_sg.add_edge(0,
0,
from_jimage=(0, 0, 0),
to_jimage=(0, 1, 0))
self.square_sg.add_edge(0,
0,
from_jimage=(0, 0, 0),
to_jimage=(0, -1, 0))
# body-centered square lattice for testing
structure = Structure(Lattice.tetragonal(5.0, 50.0), ['H', 'He'],
[[0, 0, 0], [0.5, 0.5, 0.5]])
self.bc_square_sg = StructureGraph.with_empty_graph(
structure, edge_weight_name="", edge_weight_units="")
self.bc_square_sg.add_edge(0,
0,
from_jimage=(0, 0, 0),
to_jimage=(1, 0, 0))
self.bc_square_sg.add_edge(0,
0,
from_jimage=(0, 0, 0),
to_jimage=(-1, 0, 0))
self.bc_square_sg.add_edge(0,
0,
from_jimage=(0, 0, 0),
to_jimage=(0, 1, 0))
self.bc_square_sg.add_edge(0,
0,
from_jimage=(0, 0, 0),
to_jimage=(0, -1, 0))
self.bc_square_sg.add_edge(0,
1,
from_jimage=(0, 0, 0),
to_jimage=(0, 0, 0))
self.bc_square_sg.add_edge(0,
1,
from_jimage=(0, 0, 0),
to_jimage=(-1, 0, 0))
self.bc_square_sg.add_edge(0,
1,
from_jimage=(0, 0, 0),
to_jimage=(-1, -1, 0))
self.bc_square_sg.add_edge(0,
1,
from_jimage=(0, 0, 0),
to_jimage=(0, -1, 0))
# body-centered square lattice for testing
# directions reversed, should be equivalent to as bc_square
structure = Structure(Lattice.tetragonal(5.0, 50.0), ['H', 'He'],
[[0, 0, 0], [0.5, 0.5, 0.5]])
self.bc_square_sg_r = StructureGraph.with_empty_graph(
structure, edge_weight_name="", edge_weight_units="")
self.bc_square_sg_r.add_edge(0,
0,
from_jimage=(0, 0, 0),
to_jimage=(1, 0, 0))
self.bc_square_sg_r.add_edge(0,
0,
from_jimage=(0, 0, 0),
to_jimage=(-1, 0, 0))
self.bc_square_sg_r.add_edge(0,
0,
from_jimage=(0, 0, 0),
to_jimage=(0, 1, 0))
self.bc_square_sg_r.add_edge(0,
0,
from_jimage=(0, 0, 0),
to_jimage=(0, -1, 0))
self.bc_square_sg_r.add_edge(0,
1,
from_jimage=(0, 0, 0),
to_jimage=(0, 0, 0))
self.bc_square_sg_r.add_edge(1,
0,
from_jimage=(-1, 0, 0),
to_jimage=(0, 0, 0))
self.bc_square_sg_r.add_edge(1,
0,
from_jimage=(-1, -1, 0),
to_jimage=(0, 0, 0))
self.bc_square_sg_r.add_edge(1,
0,
from_jimage=(0, -1, 0),
to_jimage=(0, 0, 0))
# MoS2 example, structure graph obtained from critic2
# (not ground state, from mp-1023924, single layer)
stdout_file = os.path.join(
os.path.dirname(__file__), "..", "..", "..",
'test_files/critic2/MoS2_critic2_stdout.txt')
with open(stdout_file, 'r') as f:
reference_stdout = f.read()
self.structure = Structure.from_file(
os.path.join(os.path.dirname(__file__), "..", "..", "..",
'test_files/critic2/MoS2.cif'))
c2o = Critic2Output(self.structure, reference_stdout)
self.mos2_sg = c2o.structure_graph(edge_weight="bond_length",
edge_weight_units="Å")
latt = Lattice.cubic(4.17)
species = ["Ni", "O"]
coords = [[0, 0, 0], [0.5, 0.5, 0.5]]
self.NiO = Structure.from_spacegroup(225, latt, species,
coords).get_primitive_structure()
def elongated_tetragonal():
lattice = Lattice.tetragonal(a=1, c=3 * sqrt(2))
coords = [[0.0, 0.0, 0.0]]
return IStructure(lattice=lattice, species=["H"], coords=coords)
def tetra_close_to_cubic():
lattice = Lattice.tetragonal(1.001 * 10 / sqrt(2), 10)
coords = [[0.0, 0.0, 0.0]]
return IStructure(lattice=lattice, species=["H"], coords=coords)
