def test_POAV_angles(self):
atoms = \
generate_atoms(generator_class='SWNTGenerator', n=10, m=0, nz=2)
# atoms.NNrc = 2.0
atoms.assign_unique_ids()
atoms.compute_POAVs()
for i, atom in enumerate(atoms):
print('atom{}: {}'.format(atom.id, atom))
for POAV in ('POAV1', 'POAV2', 'POAVR'):
if getattr(atom, POAV) is not None:
atom_POAV = getattr(atom, POAV)
sigma_pi_angles = np.degrees(atom_POAV.sigma_pi_angles)
assert_false(np.all(np.isclose(sigma_pi_angles,
3 * [np.nan],
equal_nan=True)))
print('atom{}.{}.sigma_pi_angles:\n{}'.format(
atom.id, POAV, sigma_pi_angles))
pyramidalization_angles = \
np.degrees(atom_POAV.pyramidalization_angles)
print('atom{}.{}.pyramidalization_angles:\n{}'.format(
atom.id, POAV, pyramidalization_angles))
assert_false(np.all(np.isclose(pyramidalization_angles,
3 * [np.nan],
equal_nan=True)))
misalignment_angles = \
np.degrees(atom_POAV.misalignment_angles)
print('atom{}.{}.misalignment_angles:\n{}\n'.format(
atom.id, POAV, misalignment_angles))
assert_false(np.all(np.isclose(misalignment_angles,
3 * [np.nan],
equal_nan=True)))
def test_POAV_angles(self):
atoms = \
generate_atoms(generator_class='SWNTGenerator', n=10, m=0, nz=2)
# atoms.NNrc = 2.0
atoms.assign_unique_ids()
atoms.compute_POAVs()
for i, atom in enumerate(atoms):
print('atom{}: {}'.format(atom.id, atom))
for POAV in ('POAV1', 'POAV2', 'POAVR'):
if getattr(atom, POAV) is not None:
atom_POAV = getattr(atom, POAV)
sigma_pi_angles = np.degrees(atom_POAV.sigma_pi_angles)
assert_false(
np.all(
np.isclose(sigma_pi_angles,
3 * [np.nan],
equal_nan=True)))
print('atom{}.{}.sigma_pi_angles:\n{}'.format(
atom.id, POAV, sigma_pi_angles))
pyramidalization_angles = \
np.degrees(atom_POAV.pyramidalization_angles)
print('atom{}.{}.pyramidalization_angles:\n{}'.format(
atom.id, POAV, pyramidalization_angles))
assert_false(
np.all(
np.isclose(pyramidalization_angles,
3 * [np.nan],
equal_nan=True)))
misalignment_angles = \
np.degrees(atom_POAV.misalignment_angles)
print('atom{}.{}.misalignment_angles:\n{}\n'.format(
atom.id, POAV, misalignment_angles))
assert_false(
np.all(
np.isclose(misalignment_angles,
3 * [np.nan],
equal_nan=True)))
def test3(self):
atoms = generate_atoms(elements='periodic_table')
atoms.assign_unique_ids()
atoms.kNN = 3
atoms_cp = atoms.copy()
assert_equal(atoms.kNN, atoms_cp.kNN)
def test3(self):
atoms = generate_atoms(elements='periodic_table')
atoms.assign_unique_ids()
atoms.kNN = 3
atoms_cp = atoms.copy()
assert_equal(atoms.kNN, atoms_cp.kNN)