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()