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()
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()