def compute_POAVs(self):
"""Compute `POAV1`, `POAV2`, `POAVR`."""
super().update_attrs()
POAV_classes = {'POAV1': POAV1, 'POAV2': POAV2, 'POAVR': POAVR}
for atom in self:
# the central atom must have 3 bonds for POAV analysis.
if atom.bonds.Nbonds == 3:
for POAV_name, POAV_class in list(POAV_classes.items()):
setattr(atom, POAV_name, POAV_class(atom.bonds))
for atom in self:
# the central atom must have 3 bonds for POAV analysis.
if atom.bonds.Nbonds == 3:
for POAV_name in ('POAV1', 'POAV2', 'POAVR'):
POAV = getattr(atom, POAV_name)
sigma_pi_angles = []
pyramidalization_angles = []
misalignment_angles = []
for bond, NN in zip(atom.bonds, atom.NN):
# first compute the pyramidalization angle
sigma_pi_angle = vec.angle(POAV.Vpi, bond.vector)
if sigma_pi_angle < np.pi / 2:
sigma_pi_angle = np.pi - sigma_pi_angle
sigma_pi_angles.append(sigma_pi_angle)
pyramidalization_angles.append(sigma_pi_angle -
np.pi / 2)
# the bonded atom must have a POAV to compute the
# misalignment angles
if getattr(NN, POAV_name) is not None:
NN_POAV = getattr(NN, POAV_name)
# compute vector that is orthogonal to the plane
# defined by the bond vector and the POAV of the
# center atom.
nvec = vec.cross(bond.vector, POAV.Vpi)
# the misalignment angle is the angle between the
# nearest neighbor's POAV and the plane defined by
# the bond vector and the POAV of the center atom,
# which is pi/2 minus the angle between
# the NN POAV and the normal vector to the plane
# computed above.
misalignment_angles.append(
np.abs(np.pi / 2 -
vec.angle(NN_POAV.Vpi, nvec)))
else:
misalignment_angles.append(np.nan)
POAV.pyramidalization_angles = pyramidalization_angles
POAV.misalignment_angles = misalignment_angles
POAV.sigma_pi_angles = sigma_pi_angles
def compute_POAVs(self):
"""Compute `POAV1`, `POAV2`, `POAVR`."""
super().update_attrs()
POAV_classes = {'POAV1': POAV1, 'POAV2': POAV2, 'POAVR': POAVR}
for atom in self:
# the central atom must have 3 bonds for POAV analysis.
if atom.bonds.Nbonds == 3:
for POAV_name, POAV_class in list(POAV_classes.items()):
setattr(atom, POAV_name, POAV_class(atom.bonds))
for atom in self:
# the central atom must have 3 bonds for POAV analysis.
if atom.bonds.Nbonds == 3:
for POAV_name in ('POAV1', 'POAV2', 'POAVR'):
POAV = getattr(atom, POAV_name)
sigma_pi_angles = []
pyramidalization_angles = []
misalignment_angles = []
for bond, NN in zip(atom.bonds, atom.NN):
# first compute the pyramidalization angle
sigma_pi_angle = vec.angle(POAV.Vpi, bond.vector)
if sigma_pi_angle < np.pi / 2:
sigma_pi_angle = np.pi - sigma_pi_angle
sigma_pi_angles.append(sigma_pi_angle)
pyramidalization_angles.append(
sigma_pi_angle - np.pi / 2)
# the bonded atom must have a POAV to compute the
# misalignment angles
if getattr(NN, POAV_name) is not None:
NN_POAV = getattr(NN, POAV_name)
# compute vector that is orthogonal to the plane
# defined by the bond vector and the POAV of the
# center atom.
nvec = vec.cross(bond.vector, POAV.Vpi)
# the misalignment angle is the angle between the
# nearest neighbor's POAV and the plane defined by
# the bond vector and the POAV of the center atom,
# which is pi/2 minus the angle between
# the NN POAV and the normal vector to the plane
# computed above.
misalignment_angles.append(np.abs(
np.pi / 2 - vec.angle(NN_POAV.Vpi, nvec)))
else:
misalignment_angles.append(np.nan)
POAV.pyramidalization_angles = pyramidalization_angles
POAV.misalignment_angles = misalignment_angles
POAV.sigma_pi_angles = sigma_pi_angles
def angles(self):
""":class:`~numpy:numpy.ndarray` of `Bond` pair angles."""
return np.asarray([
vec.angle(b1.vector, b2.vector) for (b1, b2) in cyclic_pairs(self)
])
def angles(self):
""":class:`~numpy:numpy.ndarray` of `Bond` pair angles."""
return np.asarray([vec.angle(b1.vector, b2.vector) for (b1, b2) in
cyclic_pairs(self)])
def test15():
u = Vector([1, 0])
v = Vector([1, 1])
assert_almost_equal(vec.angle(u, v), np.pi / 4)
def test15():
u = Vector([1, 0])
v = Vector([1, 1])
assert_almost_equal(vec.angle(u, v), np.pi/4)
