def test_molecule_R():
a1 = Atom(H, 0, 0, 0)
a2 = Atom(H, 1, 0, 0)
m = Molecule([a1, a2])
expected = [[0, 1], [1, 0]]
assert np.allclose(m.R, expected, atol=1e-10)
def test_molecule_from_xyz():
expected = Molecule([Atom(Li, 3.0, 4.0, 5.0), Atom(H, 2.3, 1.3, -1.0)])
xyz = """first line not needed
second is comment and ignored
3 3.0 4.0 5.0
1 2.3 1.3 -1.0
"""
assert Molecule.from_xyz(xyz) == expected
def test_molecule_coords():
a1 = Atom(H, -1, 0, 0)
a2 = Atom(H, 1, 0, 0)
m = Molecule([a1, a2])
expected = [[-1, 0, 0], [1, 0, 0]]
assert np.allclose(m.coords, expected, atol=1e-10)
def test_extended_huckel_hamiltonian_if_s_orthogonal():
S = np.eye(2)
m = Molecule([Atom(C, 0, 0, 0), Atom(N, 0, 0, 0)])
h = ExtendedHuckelHamiltonian(S=S, molecule=m).matrix()
assert is_diagonal(h)
assert h[0, 0] == -C.voie
assert h[1, 1] == -N.voie
def test_molecule_translated():
a1 = Atom(H, 20, 0, 0)
a2 = Atom(H, 10, 0, 0)
m = Molecule([a1, a2])
e1 = Atom(H, 20, 10, -3)
e2 = Atom(H, 10, 10, -3)
expected = Molecule([e1, e2])
assert m.translated(y=10, z=-3) == expected
def test_extended_huckel_hamiltonian_s_ones():
S = np.ones((2, 2))
m = Molecule([Atom(C, 0, 0, 0), Atom(N, 0, 0, 0)])
h = ExtendedHuckelHamiltonian(S=S, molecule=m).matrix()
assert h[0, 0] == -C.voie
assert h[1, 1] == -N.voie
expected = 1.75 * (-C.voie + -N.voie) / 2.0
assert isclose(h[1, 0], expected)
assert isclose(h[0, 1], expected)
def test_rotate():
atom = Atom(H, 0, 2, 0)
r = atom.rotation_matrix_to(x=4, y=0, z=0)
rotated = atom.rotated(r)
expected = Atom(H, 2, 0, 0)
assert rotated == expected
m = Molecule([atom])
assert m.with_atom_aligned_to(atom, x=1.0, y=0.0, z=0.0) == Molecule([expected])
assert m.rotated_about_z(np.pi / 2) == Molecule(atoms=[Atom(H, -2.0, 0.0, 0.0)])
def test_molecule_mass():
a1 = Atom(3, 0, 0, 0)
a2 = Atom(25, 1, 0, 0)
m = Molecule([a1, a2])
assert m.mass == 28
def test_molecule_sorted():
m = Molecule([Atom(Li, 1, 1, 1), Atom(H, -1, 10, -30)])
expected = Molecule([Atom(H, -1, 10, -30), Atom(Li, 1, 1, 1)])
assert m.sorted(lambda a: a.z) == expected
assert m.sorted(lambda a: a.mass) == expected
def test_atom_rotated():
a = Atom(H, 0.0, 2.0, 0.0)
r = a.rotation_matrix_to(1, 0, 0)
assert a.rotated(r) == Atom(H, 2.0, 0.0, 0.0)
def test_atom_scaled():
a = Atom(H, 1, 2, 4)
assert a.scaled(2.0) == Atom(H, 2.0, 4.0, 8.0)
def test_center_of_mass():
a1 = Atom(H, -1, 0, 0)
a2 = Atom(H, 1, 0, 0)
m = Molecule([a1, a2])
assert allclose(m.center_of_mass, (0, 0, 0))
def test_molecule___len__():
a1 = Atom(H, -1, 0, 0)
a2 = Atom(H, 1, 0, 0)
m = Molecule([a1, a2])
assert len(m) == 2
def test_molecule_rotated_about_y():
a1 = Atom(H, 1, 2, 0)
a2 = Atom(H, 0, 6, -1)
m = Molecule([a1, a2])
expected = Molecule([Atom(H, 0, 2, 1), Atom(H, 1, 6, 0)])
assert m.rotated_about_y(np.pi / 2) == expected
def test_molecule_rotated_about_z():
a1 = Atom(H, -1, 0, 100)
a2 = Atom(H, 0, -1, 200)
m = Molecule([a1, a2])
expected = Molecule([Atom(H, 0, -1, 100), Atom(H, 1, 0, 200)])
assert m.rotated_about_z(np.pi / 2) == expected
def test_molecule_rotated_raises_if_wrong_shape():
with raises(ValueError):
Molecule([Atom(H, 1, 1, 1)]).rotated(np.array([1]))
def test_atom_translated():
a = Atom(H, 1, 2, 3)
assert a.translated(x=2.0, y=3.0, z=4.0) == Atom(H, 3.0, 5.0, 7.0)
def test_atom__init__():
h1 = Atom("H", 0, 0, 0)
h2 = Atom(H, 0, 0, 0)
assert h1 == h2
def test_molecule_flipped_x():
m = Molecule([Atom(Li, 1, 1, 1), Atom(H, -1, 10, -30)])
expected = Molecule([Atom(Li, -1, 1, 1), Atom(H, 1, 10, -30)])
assert m.flipped_x() == expected
def with_atom_aligned_to(self, atom: Atom, x: float, y: float,
z: float) -> "Molecule":
r = atom.rotation_matrix_to(x=x, y=y, z=z)
return self.rotated(r)
def from_xyz(xyz: str) -> "Molecule":
"""Create a molecule from an xyz-file formatted string"""
text = (line.split() for line in xyz.splitlines()[2:] if line.strip())
atoms = [Atom(element=e, x=x, y=y, z=z) for e, x, y, z in text]
return Molecule(atoms)
def test_extended_huckel_hamiltonian_raises_if_missing_voie():
m = Molecule([Atom(Uuo, 0, 0, 0)])
S = np.eye(1)
with raises(ValueError):
ExtendedHuckelHamiltonian(S, m)
def test_molecule_com_as_origin():
m = Molecule([Atom(Li, 23, 1, 2), Atom(H, 24, 8, -23)])
translated = m.com_as_origin()
assert allclose(translated.center_of_mass, (0, 0, 0))
def test_molecule_rotated_about_x():
a1 = Atom(H, 5, 1, 0)
a2 = Atom(H, 2, 0, 1)
m = Molecule([a1, a2])
expected = Molecule([Atom(H, 5, 0, -1), Atom(H, 2, 1, 0)])
assert m.rotated_about_x(-np.pi / 2) == expected
def test_molecule_scaled():
m = Molecule([Atom(Li, 1, 1, 1), Atom(H, -1, 10, -30)])
expected = Molecule([Atom(Li, 10, 10, 10), Atom(H, -10, 100, -300)])
assert m.scaled(10) == expected
def test_atom_mass():
assert Atom(H, 0, 0, 0).mass == 1
for i in range(1, 100):
assert Atom(i, 0, 0, 0).mass == i