def make_cent(cent, weight, coords):
points = np.array([]).reshape(0,3)
if weight > 0 and weight <= 1:
weights = [weight] + [(1 - weight)/ (len(cent) - 1)] * (len(cent) - 1)
else:
weights = None
for idx in cent:
points = np.vstack((points, coords[idx]))
if u.verbosity >= 2:
if len(cent) == 1:
print(" Application point defined in atom %s." % ', '.join(u.compact_extended_list(cent, 1)))
elif len(cent) > 1 and weight > 0:
print(" Application point defined in the geometrical center of atoms %s with\n \
weight %4.2f on atom %s." % (', '.join(u.compact_extended_list(cent, 1)), weight, cent[0] + 1))
elif len(cent) > 1:
print(" Application point defined in the geometrical center of atoms %s." % \
', '.join(u.compact_extended_list(cent, 1)))
return np.average(points, axis=0, weights=weights)
def make_dipo(dipole, dipole_types, coords):
dip_type = dipole[0]
dip_s = np.sqrt(dipole_types[dip_type][0])
dip_ori = dipole[1:]
# Orient dipole along an interatomic axis
if len(dip_ori) == 2:
# -1 to adapt to Python numeration
a = coords[dip_ori[0] - 1]
b = coords[dip_ori[1] - 1]
direction = (b - a) / np.linalg.norm(b - a)
# dip = dip_s * direction
dip = direction
if u.verbosity >= 2:
print(" Dipole oriented along %s." % ', '.join(u.compact_extended_list(dip_ori)))
# Orient dipole along an interatomic axis and forming and angle
# theta with the plane defined by 3 atoms
elif len(dip_ori) == 4:
# -1 to adapt to Python numeration
a = coords[dip_ori[0] - 1]
b = coords[dip_ori[1] - 1]
c = coords[dip_ori[2] - 1]
theta = dip_ori[3]
# Generate a reference frame from point a, b, c
# Our desired direction is b - a, i.e. the x axis
# of this new ref frame. (see refframe function in
# util.py
ref = u.refframe(a, b, c)
cartesian = np.eye(3)
# Define transformation matrices
T = np.dot(cartesian, ref.T)
Ry = u.rot_mat_y(theta)
# Ry is 4x4, reduce it to 3x3
Ry = Ry[:3,:3]
x = cartesian[0]
direction = np.dot(x, Ry)
direction = np.dot(direction, T.T)
# dip = dip_s * direction
dip = direction
if u.verbosity >= 2:
print(" Dipole oriented out of the plane defined by %s by %5.2f degrees." % \
(', '.join(u.compact_extended_list(dip_ori[:-1])), theta))
else:
print(u.banner(text='ERROR', ch='#', length=80))
print("Unrecognized number of parameters for dipole orientation.")
print
sys.exit()
return dip
