def test_rotate_euler():
from math import sqrt
from ase import Atoms
d = 1.14
a = Atoms('CO', [(0, 0, 0), (d, 0, 0)])
a.euler_rotate(phi=90, theta=45, psi=180)
for p in a[0].position:
assert p == 0.0
assert abs(a[1].position[0]) < 1e-15
d2 = d / sqrt(2)
assert abs(a[1].position[1] - d2) < 1e-15
assert abs(a[1].position[2] - d2) < 1e-15
from math import sqrt
from ase import Atoms
d = 1.14
a = Atoms('CO', [(0, 0, 0), (d, 0, 0)])
a.euler_rotate(phi=90, theta=45, psi=180)
for p in a[0].position:
assert p == 0.0
assert abs(a[1].position[0]) < 1e-15
d2 = d / sqrt(2)
assert abs(a[1].position[1] - d2) < 1e-15
assert abs(a[1].position[2] - d2) < 1e-15
# Fill up HCP lattice until N z_coords
count = 0
for l in range(layers):
for i in range(int(np.ceil(np.sqrt(n)))):
for j in range(int(np.ceil(np.sqrt(n)))):
if count >= N:
break
# Randomise angles
phi = 180.*random()
theta = 180.*random()
psi = 180.*random()
# Arrange in HCP arrangement with minor random x and y displacement
x = h2o_xy * (i - 0.01*(random() - 0.5)*0 + (1+(-1)**j+(-1)**l)/4.)
y = h2o_xy * (j - 0.01*(random() - 0.5)*0 + (1+(-1)**l)/4.)
z = c / 2. + ((1. - layers) / 2. + l) * h2o_z
offset = np.array([x, y, z])
h2o = Atoms('OH2', positions=pos+offset)
Atoms.euler_rotate(h2o, phi, theta, psi,
center=h2o.get_center_of_mass())
atoms += h2o
count += 1
atoms.set_cell([a, a, c])
atoms.set_pbc(1)
io.write('test.xyz', atoms)
io.write('test.pdb', atoms)