def reduced_coordinates_displace(stepsize,
lattice_matrix,
coords,
indices=None):
"""uniform random displacement of reduced coordinates
Parameters
----------
coords : array like x(:,3)
coordinates
indices : list, optional
list of coordinates to displace, None for all coordinates in array
"""
coords = coords.reshape(-1, 3)
ilattice = vec3.invert3x3(lattice_matrix) # inverse_lattice
if indices is not None:
for i in indices:
coords[i] += np.dot(
ilattice,
stepsize * rotations.vector_random_uniform_hypersphere(3))
return
for x in coords:
x += np.dot(ilattice,
stepsize * rotations.vector_random_uniform_hypersphere(3))
def test_invert3x3(self):
q = rotations.random_q()
mx = rotations.q2mx(q)
mxi1 = invert3x3(mx)
mxi2 = np.linalg.inv(mx)
self.assertEqual(mxi1.shape, mxi2.shape)
for v1, v2 in izip(mxi1.reshape(-1), mxi2.reshape(-1)):
self.assertAlmostEqual(v1, v2, places=5)
def test_invert3x3(self):
q = rotations.random_q()
mx = rotations.q2mx(q)
mxi1 = invert3x3(mx)
mxi2 = np.linalg.inv(mx)
self.assertEqual(mxi1.shape, mxi2.shape)
for v1, v2 in zip(mxi1.reshape(-1), mxi2.reshape(-1)):
self.assertAlmostEqual(v1, v2, places=5)
def reduced_coordinates_displace(stepsize, lattice_matrix, coords, indices=None):
"""uniform random displacement of reduced coordinates
Parameters
----------
coords : array like x(:,3)
coordinates
indices : list, optional
list of coordinates to displace, None for all coordinates in array
"""
ilattice = vec3.invert3x3(lattice_matrix) # inverse_lattice
if indices:
for i in indices:
coords[i] += np.dot(ilattice, stepsize * rotations.vector_random_uniform_hypersphere(3))
return
for x in coords:
x += np.dot(ilattice, stepsize * rotations.vector_random_uniform_hypersphere(3))
