def test_basic_atoms():
box = [[2.715, 2.715, 0], [0, 2.715, 2.715], [2.715, 0, 2.715]]
coords = [[0, 0, 0], [0.25, 0.2, 0.25]]
elements = ["Si", "Si"]
Si = Atoms(lattice_mat=box, coords=coords, elements=elements)
dim = get_supercell_dims(Si)
assert dim == [3, 3, 3]
polar = Si.check_polar
Si.props = ["a", "a"]
vac_pad = VacuumPadding(Si)
den_2d = round(vac_pad.get_effective_2d_slab().density, 2)
den_0d = round(vac_pad.get_effective_molecule().density, 2)
den_lll_red = round(Si.get_lll_reduced_structure().density, 2)
strng = Si.get_string()
scell_nat = Si.make_supercell([2, 2, 2]).num_atoms
scell_nat2 = Si.make_supercell_matrix([[2, 0, 0], [0, 2, 0],
[0, 0, 2]]).num_atoms
# print("scell_nat,scell_nat2", scell_nat, scell_nat2)
# print(Si.make_supercell([2, 2, 2]))
# print()
# print(Si.make_supercell_matrix([[2, 0, 0], [0, 2, 0], [0, 0, 2]]))
com = round(Si.get_center_of_mass()[0], 3)
rem = (Si.make_supercell([2, 2, 2]).remove_site_by_index(site=0)).num_atoms
prim = Si.get_primitive_atoms
print(prim.cart_coords)
assert round(prim.cart_coords[0][0], 2) == round(4.37815150, 2)
# print ('raw_distance_matrix', prim.raw_distance_matrix)
# print ('raw_distance_matrix', Si.raw_distance_matrix)
# print ('distance_matrix', Si.pymatgen_converter().distance_matrix)
assert round(prim.raw_distance_matrix[0][1],
2) == round(4.42386329832851, 2)
print(prim.raw_angle_matrix)
d = Si.to_dict()
new_at = Atoms.from_dict(d)
angs_a = d["angles"][0]
Si_2_den = Atoms(
lattice_mat=d["lattice_mat"],
coords=d["coords"],
elements=d["elements"],
).density
Si_xyz = Si.get_xyz_string
Si.write_xyz(filename="atoms.xyz")
tmp = Atoms.from_xyz(filename="atoms.xyz")
cmd = 'rm atoms.xyz'
os.system(cmd)
Si.center_around_origin()
# print ('scell_nat', Si_2)
assert (
round(Si.volume, 2),
Si.atomic_numbers,
Si.num_atoms,
Si.frac_coords[0][0],
Si.cart_coords[0][0],
round(Si.density, 2),
Si.spacegroup(),
Si.pymatgen_converter() != {},
polar,
Si.props[0],
den_2d,
den_0d,
round(Si.packing_fraction, 2),
Si.composition.to_dict(),
strng != "",
den_lll_red,
scell_nat,
com,
rem,
angs_a,
round(Si_2_den, 2),
) == (
40.03,
[14, 14],
2,
0,
0.0,
2.33,
"C2/m (12)",
True,
False,
"a",
0.35,
0.01,
0.28,
{
"Si": 2
},
True,
2.33,
16,
0.679,
15,
60.0,
2.33,
)
cc = Si.center()
cc = Si.center(axis=[0, 0, 1])
m1 = Atoms.from_dict(get_jid_data("JVASP-6640")["atoms"])
assert m1.check_polar == True
print("Strain test")
print(m1)
m1.apply_strain(0.1)
print(m1)
assert m1.lattice_mat[2][2] == 32.8717576
m1.apply_strain([0, 0, 0.1])
assert m1.lattice_mat[2][2] == 36.158933360000006
filename = "atoms.cif"
m1.write_cif(filename)
a = Atoms.from_cif(filename)
filename = "POSCAR"
m1.write_poscar(filename)
m2 = Atoms.from_poscar(filename)
filename = "atoms.xyz"
m1.write_xyz(filename)
m3 = Atoms.from_xyz(filename)
cmd = "rm atoms.xyz POSCAR atoms.cif"
os.system(cmd)
def make_surface(self):
"""Generate specified surface. Modified from ase package."""
atoms = self.atoms
h_index, k_index, l_index = self.indices
h0, k0, l0 = self.indices == 0
if h0 and k0 or h0 and l0 or k0 and l0: # if two indices are zero
if not h0:
c1, c2, c3 = [(0, 1, 0), (0, 0, 1), (1, 0, 0)]
if not k0:
c1, c2, c3 = [(0, 0, 1), (1, 0, 0), (0, 1, 0)]
if not l0:
c1, c2, c3 = [(1, 0, 0), (0, 1, 0), (0, 0, 1)]
else:
p, q = ext_gcd(k_index, l_index)
a1, a2, a3 = self.atoms.lattice_mat # .lat_lengths()
# constants describing the dot product of basis c1 and c2:
# dot(c1,c2) = k1+i*k2, i in Z
k1 = np.dot(
p * (k_index * a1 - h_index * a2) + q *
(l_index * a1 - h_index * a3),
l_index * a2 - k_index * a3,
)
k2 = np.dot(
l_index * (k_index * a1 - h_index * a2) - k_index *
(l_index * a1 - h_index * a3),
l_index * a2 - k_index * a3,
)
if abs(k2) > self.tol:
i = -int(round(k1 / k2))
p, q = p + i * l_index, q - i * k_index
a, b = ext_gcd(p * k_index + q * l_index, h_index)
c1 = (p * k_index + q * l_index, -p * h_index, -q * h_index)
c2 = np.array((0, l_index, -k_index)) // abs(gcd(l_index, k_index))
c3 = (b, a * p, a * q)
lattice = atoms.lattice_mat # .lat_lengths()
basis = np.array([c1, c2, c3])
scaled = np.linalg.solve(basis.T, np.array(atoms.frac_coords).T).T
scaled -= np.floor(scaled + self.tol)
new_coords = scaled
tmp_cell = np.dot(basis, lattice)
M = np.linalg.solve(lattice, tmp_cell)
cart_coords = np.dot(scaled, lattice)
new_coords = np.dot(cart_coords, M)
new_atoms = Atoms(
lattice_mat=tmp_cell,
coords=new_coords,
elements=atoms.elements,
cartesian=True,
)
surf_atoms = new_atoms.make_supercell_matrix([1, 1, self.layers])
# print("supercell_cart_coords", surf_atoms.frac_coords)
new_lat = surf_atoms.lattice_mat # lat_lengths()
a1 = new_lat[0]
a2 = new_lat[1]
a3 = new_lat[2]
new_lat = np.array([
a1,
a2,
np.cross(a1, a2) * np.dot(a3, np.cross(a1, a2)) /
norm(np.cross(a1, a2))**2,
])
a1 = new_lat[0]
a2 = new_lat[1]
a3 = new_lat[2]
# print("a1,a2,a3", new_lat)
latest_lat = np.array([
(np.linalg.norm(a1), 0, 0),
(
np.dot(a1, a2) / np.linalg.norm(a1),
np.sqrt(
np.linalg.norm(a2)**2 -
(np.dot(a1, a2) / np.linalg.norm(a1))**2),
0,
),
(0, 0, np.linalg.norm(a3)),
])
M = np.linalg.solve(new_lat, latest_lat)
new_cart_coords = surf_atoms.cart_coords # np.dot(scaled,lattice)
new_coords = np.dot(new_cart_coords, M)
new_atoms = Atoms(
lattice_mat=latest_lat,
elements=surf_atoms.elements,
coords=new_coords,
cartesian=True,
).center_around_origin()
frac_coords = new_atoms.frac_coords
frac_coords[:] = frac_coords[:] % 1
new_atoms = Atoms(
lattice_mat=latest_lat,
elements=surf_atoms.elements,
coords=frac_coords,
cartesian=False,
)
new_lat = new_atoms.lattice_mat
new_cart_coords = new_atoms.cart_coords
elements = new_atoms.elements
new_lat[2][2] = new_lat[2][2] + self.vacuum
with_vacuum_atoms = Atoms(
lattice_mat=new_lat,
elements=elements,
coords=new_cart_coords,
cartesian=True,
)
# new_atoms.center()
# print (with_vacuum_atoms)
return with_vacuum_atoms