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_POAVs(self):
atoms = \
generate_atoms(generator_class='SWNTGenerator', n=5, m=0, nz=5)
atoms.compute_POAVs()
atoms.filter(atoms.coordination_numbers == 3)
atom = atoms[10]
assert_equals(atom.bonds.Nbonds, 3)
for POAV in ('POAV1', 'POAV2', 'POAVR'):
atom_POAV = getattr(atom, POAV)
assert_is_instance(atom_POAV, getattr(sknano.core.atoms, 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)))
pyramidalization_angles = \
np.degrees(atom_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)
assert_false(np.all(np.isclose(misalignment_angles,
3 * [np.nan],
equal_nan=True)))
print(getattr(atom, POAV))
def test7():
atoms = generate_atoms(generator_class='SWNTGenerator', n=5, m=0, nz=5)
atoms.update_attrs()
filtered = atoms.filtered_ids(list(range(5, 26)))
atoms.filter_ids(list(range(5, 26)))
assert_equal(filtered, atoms)
assert_true(atoms.Natoms, 20)
def test8():
atoms = generate_atoms(generator_class='SWNTGenerator', n=5, m=0, nz=5)
atoms.update_attrs()
filtered1 = atoms.filtered(atoms.coordination_numbers > 1)
filtered2 = atoms.filtered("coordination_numbers > 1")
atoms.filter(atoms.coordination_numbers > 1)
assert_equal(filtered1, atoms)
assert_equal(filtered1, filtered2)
def test5():
atoms = \
generate_atoms(generator_class='SWNTGenerator', n=5, m=5, nz=5,
verbose=True)
atoms.assign_unique_ids()
for i, atom in enumerate(atoms):
assert_true(atoms[i] is atoms.get_atom(atom.id))
assert_equal(i, atoms.index(atom))
def test6():
atoms = generate_atoms(generator_class='SWNTGenerator', n=3, m=3, nz=10)
atoms.assign_unique_ids()
atoms.center_centroid()
atoms.kNN = 6
atoms.NNrc = 9.0
new_atoms = atoms.filtered((atoms.z >= -5) & (atoms.z <= 5))
assert_equal(atoms.kNN, 6)
assert_equal(atoms.NNrc, 9.0)
assert_equal(atoms.kNN, new_atoms.kNN)
assert_equal(atoms.NNrc, new_atoms.NNrc)
def test_find_target_atom():
atoms = generate_atoms(generator_class='SWNTGenerator', n=10, m=10, nz=3)
atoms.center_centroid()
atoms.assign_unique_ids()
atoms.update_attrs()
target_atom = find_target_atom(atoms, target_coords=[0.0, 5.0, 0.0],
search_radius=1.0, nearest_target=True)
print('atoms.z.min(), atoms.z.max(): {}, {}'.format(
atoms.z.min(), atoms.z.max()))
print('atom_ids: {}'.format(atoms.atom_ids))
print('CNs: {}'.format(atoms.coordination_numbers))
print('target_atom: {}'.format(target_atom))
def test3():
atoms = generate_atoms(elements='periodic_table')
atoms.assign_unique_ids()
print(atoms[:5])
atoms_slice = atoms[5:10]
atoms[:5] = atoms_slice
assert_equal(atoms[:5], atoms[5:10])
print(atoms[:5])
atoms[:5] = ['C', 'H', 'N', 'Ar', 'He']
print(atoms[:8])
atoms[0] = 'Au'
print(atoms[:2])
def test5():
atoms = \
BasisAtoms(atoms=generate_atoms(elements='periodic_table').symbols)
print(atoms[:5])
atoms_slice = atoms[5:10]
atoms[:5] = atoms_slice
assert_equal(atoms[:5], atoms[5:10])
print(atoms[:5])
atoms[:5] = ['C', 'H', 'N', 'Ar', 'He']
print(atoms[:8])
atoms[0] = 'Au'
print(atoms[:2])
def test_atom_bonds(self):
atoms = \
generate_atoms(generator_class='SWNTGenerator', n=10, m=5, nz=1)
atoms.kNN = 3
atoms.NNrc = 2.0
atoms.compute_POAVs()
bonds = atoms.bonds
assert_equal(len(bonds), atoms.coordination_numbers.sum())
assert_equal(bonds.Nbonds, atoms.coordination_numbers.sum())
for i, atom in enumerate(atoms):
if atom.bonds.Nbonds > 1:
print('atom.bonds.angles:\n'
'{}'.format(np.degrees(atom.bonds.angles)))
for j, bond in enumerate(atom.bonds):
assert_true(np.allclose(bond.vector,
atom.bonds.vectors[j]))
assert_equal(bond.length, atom.bonds.lengths[j])
def test4():
atoms = generate_atoms(elements='periodic_table')
atoms.assign_unique_ids()
a1 = atoms[:10]
a2 = atoms[:5]
assert_equal(a1 + a2, atoms[:10])
a1 = atoms[:5]
a2 = atoms[:10]
assert_equal(a1 + a2, atoms[:10])
assert_equal(atoms + atoms.__atom_class__('H', id=1), atoms)
assert_equal(atoms.__atom_class__('H', id=1) + atoms, atoms)
a1 = atoms[:25]
a2 = atoms[25:]
assert_equal((a1 + a2).elements.tolist(), element_symbols)
assert_equal((a1 + a2), atoms)
def test3(self):
atoms = \
generate_atoms(generator_class='SWNTGenerator', n=10, m=0, nz=5)
atoms.kNN = 30
atoms.NNrc = 10
atoms.update_neighbors(cutoffs=[1.5, 2.5, 2.9, 3.8, 4.3])
# print(atoms.neighbors.tolist())
print(atoms.neighbor_distances.tolist())
# print('first_neighbors:\n{}'.format(atoms.first_neighbors))
# print('second_neighbors:\n{}'.format(atoms.second_neighbors))
print('len(first_neighbors): {}'.format(
[len(atom.first_neighbors) for atom in atoms]))
print('len(second_neighbors): {}'.format(
[len(atom.second_neighbors) for atom in atoms]))
print('len(third_neighbors): {}'.format(
[len(atom.third_neighbors) for atom in atoms]))
print('len(4th_neighbors): {}'.format(
[len(atom.get_neighbors(4)) for atom in atoms]))
print('len(5th_neighbors): {}'.format(
[len(atom.get_neighbors(5)) for atom in atoms]))
def test_generate_atoms():
atoms = generate_atoms(elements=element_symbols)
assert_equals(atoms.Natoms, len(element_symbols))
atoms = generate_atoms(generator_class="SWNTGenerator", n=10, m=10, nz=10)
assert_equals(atoms.Natoms, 400)
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 test4(self):
atoms = \
generate_atoms(generator_class='SWNTGenerator', n=3, m=0, nz=5)
assert_equal(compute_Natoms((3, 0), nz=5), atoms.Natoms)
assert_equal(atoms.Natoms, atoms.ids[-1])
def test2():
atoms = generate_atoms(elements='periodic_table')
atoms.assign_unique_ids()
atoms_slice = atoms[5:10]
print(atoms_slice)
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)
