def orthogonal_basis(X, Y=None):
is_1d = Y is None
b = np.zeros((3, 3))
b[0] = X
if not is_1d:
b[1] = Y
b = complete_cell(b)
Q = np.linalg.qr(b.T)[0].T
if np.dot(b[0], Q[0]) < 0:
Q[0] = -Q[0]
if np.dot(b[2], Q[1]) < 0:
Q[1] = -Q[1]
if np.linalg.det(Q) < 0:
Q[2] = -Q[2]
if is_1d:
Q = Q[[1, 2, 0]]
return Q
def test_cell_completion():
import numpy as np
from ase.geometry.cell import complete_cell
eps = 1E-10
rng = np.random.RandomState(0)
def random_unit_vector():
while 1:
v = rng.uniform(-1, 1, 3)
norm = np.linalg.norm(v)
if norm > eps:
return v / norm
for it in range(100):
cell = np.zeros((3, 3))
index = rng.randint(0, 3)
cell[index] = random_unit_vector()
complete = complete_cell(cell)
assert abs(np.linalg.norm(complete[index]) - 1) < eps
assert np.linalg.det(complete) > 0
assert np.linalg.matrix_rank(complete) == 3
def complete(self):
"""Convert missing cell vectors into orthogonal unit vectors."""
from ase.geometry.cell import complete_cell
cell = Cell(complete_cell(self.array))
cell._pbc = self._pbc.copy()
return cell
def complete(self):
"""Convert missing cell vectors into orthogonal unit vectors."""
from ase.geometry.cell import complete_cell
return Cell(complete_cell(self.array), self.pbc.copy())