def rotate(grid, alignment=p.n_subs, trend=p.n_shel, bias=p.n_bias):
''' grid-based molecule orientation rotator '''
if is_top(grid) or is_bot(grid):
grid.n = np.array(alignment)
elif is_osh(grid):
grid.n = envelope(grid, trend)
elif is_ish(grid):
grid.n = envelope(grid, trend - u.cartesian(bias))
else:
grid.n = np.array(alignment) # bulk initial condition
def __init__(self,
position=np.empty(3),
orientation=np.random.randn(3),
order_degree=0.5,
biaxiality=0):
self._r = np.array(position)
self._n = u.cartesian(np.array(orientation))
self._S = order_degree
self._P = biaxiality
self._Q = np.empty((3, 3))
self._h = np.empty((3, 3))
def evolute(mesh,
L=p.L,
A=p.A,
B=p.B,
C=p.C,
W_subs=p.W_sub,
W_shel=p.W_she,
dt=p.dt,
gamma=p.gamma):
lap_Qs = laplacian(mesh)
grad_Qs = gradient(mesh)
for x in range(p.x_nog):
for y in range(p.y_nog):
for z in range(p.z_nog):
grid = mesh[x, y, z]
lap_Q = lap_Qs[x, y, z]
grad_Q = grad_Qs[x, y, z]
if c.is_top(grid) or c.is_bot(grid): # h_surf of substrate
Q_bound = Q_tensor(p.n_subs, p.S_subs)
grid.h = h_surf(grid.Q,
grad_Q,
Q_bound=Q_bound,
surf_normal=np.array([0, 0, 1]),
W=W_subs)
elif c.is_osh(grid) or c.is_ish(grid): # h_surf of shell
Q_bound = Q_tensor(c.envelope(p.n_shel), p.S_subs)
grid.h = h_surf(grid.Q,
grad_Q,
Q_bound=Q_bound,
surf_normal=u.cartesian(grid.r),
W=W_shel)
else: # h_bulk
grid.h = h_bulk(grid.Q, lap_Q)
grid.Q += grid.h * dt / gamma - np.trace(
grid.Q) * np.eye(3) / 3 # EL modification
def n(self, value):
if 2 <= len(value) <= 3:
self._n = u.cartesian(np.array(value))
else:
raise ValueError
def envelope(grid, trend=p.n_shel):
''' calculate the orientation around the sphere under a special arrangement '''
N = u.cartesian(trend)
r = u.cartesian(grid.r)
return N - np.dot(N, r) * r