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 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 test_structure_data(self):
fname = resource_filename('sknano', 'data/nanotubes/1005_5cells.data')
swnt = SWNTGenerator(n=10, m=5, nz=5)
swnt_atoms = swnt.atoms
swnt_atoms.compute_POAVs()
data = DATAReader(fname)
atoms = data.atoms
atoms.compute_POAVs()
assert_equals(swnt_atoms.Natoms, atoms.Natoms)
def test_structure_data(self):
fname = resource_filename('sknano', 'data/nanotubes/1005_5cells.data')
swnt = SWNTGenerator(n=10, m=5, nz=5)
swnt_atoms = swnt.atoms
swnt_atoms.compute_POAVs()
data = DATAReader(fname)
atoms = data.atoms
atoms.compute_POAVs()
assert_equals(swnt_atoms.Natoms, atoms.Natoms)
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 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 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)))