def rotate_orbital(self, phi=0, theta=0, psi=0):
old_axes = get_rotation_axes(*self.orientation[:2])
new_axes = get_rotation_axes(phi, theta)
for item in chain(self.bonds, self.mesh):
# Undo current orientation
self._rotate_item(item, old_axes, *self.orientation, backward=True)
# Actuallly rotate to new orientation
self._rotate_item(item, new_axes, phi, theta, psi, backward=False)
self.orientation = [phi, theta, psi]
def rotate_molecule(self,
phi=0,
theta=0,
psi=0): # Rotate using Euler angles phi, theta, psi
old_phi = self.phi
old_theta = self.theta
old_psi = self.psi
# first rotate items back to original orientation
axes = get_rotation_axes(old_phi, old_theta)
for item in self.items:
item.rotate(old_psi,
axes[2][0],
axes[2][1],
axes[2][2],
local=True) # first undo psi-rotation
item.rotate(old_theta,
axes[1][0],
axes[1][1],
axes[1][2],
local=True) # next undo theta-rotation
item.rotate(old_phi,
axes[0][0],
axes[0][1],
axes[0][2],
local=True) # finally undo phi-rotation
# now rotate items to new desired orientation
axes = get_rotation_axes(phi, theta)
for item in self.items:
item.rotate(-phi, axes[0][0], axes[0][1], axes[0][2],
local=True) # first do phi-rotation
item.rotate(-theta, axes[1][0], axes[1][1], axes[1][2],
local=True) # next do theta-rotation
item.rotate(-psi, axes[2][0], axes[2][1], axes[2][2],
local=True) # finally do psi-rotation
self.phi = phi
self.theta = theta
self.psi = psi
return
def _refresh_mesh(self):
if self.mesh is not None:
self.removeItem(self.mesh)
self.mesh = None
if self.orbital is None:
return
data = self.orbital.psik['data']
self.mesh = self._get_iso_mesh(data)
self.addItem(self.mesh)
# Updating the mesh after iso val change would leave it
# unrotated
axes = get_rotation_axes(*self.orientation[:2])
self._rotate_item(self.mesh, axes, *self.orientation, backward=False)
def _refresh_mesh(self):
if self.mesh:
for mesh in self.mesh:
self.removeItem(mesh)
self.mesh = []
if self.orbital is None or not self.options.is_show_mesh():
return
data = self.orbital.psi['data']
plus_mesh = self._get_iso_mesh(data, 'red', 1)
minus_mesh = self._get_iso_mesh(data, 'blue', -1)
self.addItem(plus_mesh)
self.addItem(minus_mesh)
self.mesh = [plus_mesh, minus_mesh]
# Updating the mesh after iso val change would leave it
# unrotated
axes = get_rotation_axes(*self.orientation[:2])
for item in self.mesh:
self._rotate_item(item, axes, *self.orientation, backward=False)