def test_methanol(self):
"""Test for topology computation."""
methanol = BondedAtoms(molecule("CH3OH"))
# confirm atomic numbers
self.assertTrue(
np.allclose(methanol.get_atomic_numbers(),
np.array([6, 8, 1, 1, 1, 1])))
# confirm O-H distance
self.assertTrue(np.allclose(methanol.get_distance(1, 3), 0.97))
bond_list = [(0, 1), (0, 2), (0, 4), (0, 5), (1, 3)]
for t in bond_list:
methanol.add_bond(*t)
# bonds are calculated correctly?
self.assertEqual(set(tuple(b) for b in methanol.get_bonded_bonds()),
{(0, 1), (1, 3), (0, 5), (0, 4), (0, 2)})
# angles are calculated correctly?
self.assertEqual(
set(tuple(a) for a in methanol.get_bonded_angles()), {(1, 0, 2),
(1, 0, 4),
(1, 0, 5),
(2, 0, 4),
(2, 0, 5),
(4, 0, 5),
(0, 1, 3)})
# dihedrals are calculated correctly?
dihedrals_ref = {(2, 0, 1, 3), (4, 0, 1, 3), (5, 0, 1, 3)}
for d in methanol.get_bonded_dihedrals():
if tuple(d) in dihedrals_ref:
dihedrals_ref.remove(tuple(d))
elif tuple(d[::-1]) in dihedrals_ref:
dihedrals_ref.remove(tuple(d[::-1]))
self.assertTrue(len(dihedrals_ref) == 0)
# impropers are calculated correctly?
self.assertEqual(
set(tuple(i) for i in methanol.get_bonded_impropers()),
{(0, 1, 2, 4), (0, 1, 2, 5), (0, 1, 4, 5), (0, 2, 4, 5)})
def test_casting(self):
"""Test for down-casting from ``ase.Atoms`` to BondedAtoms."""
atoms = molecule("CH3CH2OH")
bonded_atoms = BondedAtoms(atoms)
# the instance is BondedAtoms?
self.assertTrue(isinstance(bonded_atoms, BondedAtoms))
# 'bonds' property has been created?
self.assertTrue("bonds" in bonded_atoms.arrays)
# 'types' property has been created?
self.assertTrue("types" in bonded_atoms.arrays)
# all data except for 'bonds' stays unchanged?
self.assertTrue(
all(
np.allclose(v, atoms.arrays[k])
for k, v in bonded_atoms.arrays.items()
if k not in ["bonds", "types"]))
def test_gold(self):
"""Test for basic operations."""
a = 4.05 # gold lattice constant
b = a / 2
au = BondedAtoms("Au",
cell=[(0, b, b), (b, 0, b), (b, b, 0)],
pbc=True)
# initial types are 1?
self.assertTrue(np.allclose(au.get_types(), np.ones(len(au))))
au.add_bond(0, 0, img2=(1, 0, 0))
# a bond is added?
self.assertTrue(
np.allclose(
au.get_bonds(),
[[[0, 1, 0, 0], [0, -1, 0, 0], [0, 0, 0, 0], [0, 0, 0, 0]]]))
# multiplying and repeating give the same result?
self.assertTrue(
np.allclose((au * (2, 2, 2)).get_bonds(),
au.repeat((2, 2, 2)).get_bonds()))
chain = au * (3, 1, 1)
# types are correctly copied?
self.assertTrue(np.allclose(chain.get_types(), np.ones(len(chain))))
chain.change_max_bonds(2)
# the maximum number of bonds per atoms can be reduced?
self.assertTrue(
np.allclose(
chain.get_bonds(),
[[[1, 0, 0, 0], [2, -1, 0, 0]], [[1, 0, 0, 0], [-1, 0, 0, 0]],
[[-2, 1, 0, 0], [-1, 0, 0, 0]]]))
chain.remove_bond(0, 2, img2=(-1, 0, 0))
# a specified bond is removed?
self.assertTrue(
np.allclose(
chain.get_bonds(),
[[[1, 0, 0, 0], [0, 0, 0, 0]], [[1, 0, 0, 0], [-1, 0, 0, 0]],
[[-1, 0, 0, 0], [0, 0, 0, 0]]]))
chain.set_types([1, 2, 3])
# types are correctly set?
self.assertTrue(np.allclose(chain.get_types(), [1, 2, 3]))
del chain[2]
# a specified atom is deleted?
self.assertTrue(np.allclose(chain.get_types(), [1, 2]))
chain.change_max_bonds(4)
# the maximum number of bonds per atoms can be increased?
self.assertTrue(
np.allclose(
chain.get_bonds(),
[[[1, 0, 0, 0], [0, 0, 0, 0], [0, 0, 0, 0], [0, 0, 0, 0]],
[[-1, 0, 0, 0], [0, 0, 0, 0], [0, 0, 0, 0], [0, 0, 0, 0]]]))
def test_wrapping(self):
"""Test for ``BondedAtoms.wrap()``."""
atoms = BondedAtoms(molecule("CH3CH2OCH3"))
positions = atoms.get_positions()
bonded_pairs = [
(i, j) for i, j in itertools.combinations(range(len(atoms)), 2)
if np.linalg.norm(positions[i] - positions[j]) < 1.55
]
# there are eleven bonds in CH3CH2OCH3
self.assertEqual(len(bonded_pairs), 11)
bond_lengths = sorted(
atoms.get_distance(*pair) for pair in bonded_pairs)
for t in bonded_pairs:
atoms.add_bond(*t)
def get_bond_length(atoms):
bond_array = atoms.get_bonds()
cell = atoms.get_cell()
positions = atoms.get_positions()
return sorted(
np.linalg.norm((cell * bond[1:]).sum(axis=0) +
positions[i + bond[0]] - positions[i])
for i, bonds in enumerate(bond_array) for bond in bonds
if 0 < bond[0])
# bond length is correct before wrapping?
self.assertTrue(np.allclose(bond_lengths, get_bond_length(atoms)))
atoms.set_cell([[5., 0., 0.], [0., 5., 0.], [0., 0., 5.]])
atoms.set_pbc(True)
atoms.wrap()
# bond length is correct after wrapping?
self.assertTrue(np.allclose(bond_lengths, get_bond_length(atoms)))
def test_methanol(self):
"""Test for equivalence between original and written/read data."""
atoms = BondedAtoms(molecule("CH3OH"))
# confirm atomic numbers
self.assertTrue(
np.allclose(atoms.get_atomic_numbers(),
np.array([6, 8, 1, 1, 1, 1])))
# confirm O-H distance
self.assertTrue(np.allclose(atoms.get_distance(1, 3), 0.97))
atoms.set_types([1, 2, 3, 4, 3, 3])
positions = atoms.get_positions()
bonded_pairs = [
(i, j) for i, j in itertools.combinations(range(len(atoms)), 2)
if np.linalg.norm(positions[i] - positions[j]) < 1.5
]
# there are five bonds in CH3OH
self.assertEqual(len(bonded_pairs), 5)
for pair in bonded_pairs:
atoms.add_bond(*pair)
atoms.sort_bonds()
atoms.set_cell([[5., 0., 0.], [0., 5., 0.], [0., 0., 5.]])
atoms.center()
write_files(atoms)
atoms_from_data = create_atoms_from_data("data.tmp", "molecular")
atoms_from_molecule = create_atoms_from_molecule("molecule.tmp")
# atoms from Lammps' data and molecule file must be eaqual.
self.assertTrue(
np.allclose(atoms_from_data.get_positions(),
atoms_from_molecule.get_positions()))
self.assertTrue(
np.allclose(atoms_from_data.get_masses(),
atoms_from_molecule.get_masses()))
self.assertTrue(
np.allclose(atoms_from_data.get_types(),
atoms_from_molecule.get_types()))
self.assertTrue(
np.allclose(atoms_from_data.get_bonds(),
atoms_from_molecule.get_bonds()))
# comparison with original atoms
self.assertTrue(
np.allclose(atoms_from_data.get_positions(),
atoms.get_positions()))
self.assertTrue(
np.allclose(atoms_from_data.get_masses(), atoms.get_masses()))
self.assertTrue(
np.allclose(atoms_from_data.get_types(), atoms.get_types()))
# storing order of bonds might be changed
atoms_from_data.sort_bonds()
self.assertTrue(
np.allclose(atoms_from_data.get_bonds(), atoms.get_bonds()))
remove_files()
def test_nacl(self):
"""Test for equivalence between original and written/read data."""
atoms = BondedAtoms(bulk("NaCl", "rocksalt", a=5.64,
orthorhombic=True))
# confirm atomic numbers
self.assertTrue(
np.allclose(atoms.get_atomic_numbers(), np.array([11, 17, 11,
17])))
atoms.set_types([1, 2, 1, 2])
atoms.change_max_bonds(6)
cell = atoms.get_cell()
positions = atoms.get_positions()
for i, j in itertools.combinations(range(len(atoms)), 2):
r_original = positions[j] - positions[i]
for ix, iy, iz in itertools.product(*[(-1, 0, 1)] * 3):
r = r_original + ix * cell[0] + iy * cell[1] + iz * cell[2]
if np.isclose(np.linalg.norm(r), 2.82):
atoms.add_bond(i, j, img2=(ix, iy, iz))
atoms *= 5
atoms.sort_bonds()
write_files(atoms)
atoms_from_data = create_atoms_from_data("data.tmp",
"molecular",
pbc=True)
# comparison with original atoms
self.assertTrue(
np.allclose(atoms_from_data.get_positions(),
atoms.get_positions()))
self.assertTrue(
np.allclose(atoms_from_data.get_masses(), atoms.get_masses()))
self.assertTrue(
np.allclose(atoms_from_data.get_types(), atoms.get_types()))
# storing order of bonds might be changed
atoms_from_data.sort_bonds()
self.assertTrue(
np.allclose(atoms_from_data.get_bonds(), atoms.get_bonds()))
remove_files()