def run():
tol = 1E-14
rng = np.random.RandomState(0)
cell = Cell(
[[8.972058879514716, 0.0009788104586639142, 0.0005932485724084841],
[4.485181755775297, 7.770520334862034, 0.00043663339838788054],
[4.484671994095723, 2.5902066679984634, 16.25695615743613]])
cell.minkowski_reduce()
for i in range(40):
B = rng.uniform(-1, 1, (3, 3))
R, H = minkowski_reduce(B)
assert np.allclose(H @ B, R, atol=tol)
assert np.sign(np.linalg.det(B)) == np.sign(np.linalg.det(R))
norms = np.linalg.norm(R, axis=1)
assert (np.argsort(norms) == range(3)).all()
# Test idempotency
_, _H = minkowski_reduce(R)
assert (_H == np.eye(3).astype(np.int)).all()
rcell, _ = Cell(B).minkowski_reduce()
assert np.allclose(rcell, R, atol=tol)
cell = np.array([[1, 1, 2], [0, 1, 4], [0, 0, 1]])
unimodular = np.array([[1, 2, 2], [0, 1, 2], [0, 0, 1]])
assert np.linalg.det(unimodular) == 1
lcell = unimodular.T @ cell
# test 3D
rcell, op = minkowski_reduce(lcell)
assert np.linalg.det(rcell) == 1
for pbc in [1, True, (1, 1, 1)]:
rcell, op = minkowski_reduce(lcell, pbc=pbc)
assert np.linalg.det(rcell) == 1
assert np.sign(np.linalg.det(rcell)) == np.sign(np.linalg.det(lcell))
# test 0D
rcell, op = minkowski_reduce(lcell, pbc=[0, 0, 0])
assert (rcell == lcell).all() # 0D reduction does nothing
# test 1D
for i in range(3):
rcell, op = minkowski_reduce(lcell, pbc=np.roll([1, 0, 0], i))
assert (rcell == lcell).all() # 1D reduction does nothing
zcell = np.zeros((3, 3))
zcell[0] = lcell[0]
rcell, _ = Cell(zcell).minkowski_reduce()
assert np.allclose(rcell, zcell, atol=tol)
# test 2D
for i in range(3):
pbc = np.roll([0, 1, 1], i)
rcell, op = minkowski_reduce(lcell.astype(np.float), pbc=pbc)
assert (rcell[i] == lcell[i]).all()
zcell = np.copy(lcell.astype(np.float))
zcell[i] = 0
rzcell, _ = Cell(zcell).minkowski_reduce()
rcell[i] = 0
assert np.allclose(rzcell, rcell, atol=tol)
import numpy as np
from ase.geometry import minkowski_reduce
from ase.cell import Cell
tol = 1E-14
rng = np.random.RandomState(0)
np.seterr(all='raise')
cell = Cell([[8.972058879514716, 0.0009788104586639142, 0.0005932485724084841],
[4.485181755775297, 7.770520334862034, 0.00043663339838788054],
[4.484671994095723, 2.5902066679984634, 16.25695615743613]])
cell.minkowski_reduce()
for i in range(40):
B = rng.uniform(-1, 1, (3, 3))
R, H = minkowski_reduce(B)
assert np.allclose(H @ B, R, atol=tol)
assert np.sign(np.linalg.det(B)) == np.sign(np.linalg.det(R))
norms = np.linalg.norm(R, axis=1)
assert (np.argsort(norms) == range(3)).all()
# Test idempotency
_, _H = minkowski_reduce(R)
assert (_H == np.eye(3).astype(np.int)).all()
rcell, _ = Cell(B).minkowski_reduce()
assert np.allclose(rcell, R, atol=tol)
cell = np.array([[1, 1, 2], [0, 1, 4], [0, 0, 1]])
unimodular = np.array([[1, 2, 2], [0, 1, 2], [0, 0, 1]])
def test_issue():
x = [[8.972058879514716, 0.0009788104586639142, 0.0005932485724084841],
[4.485181755775297, 7.770520334862034, 0.00043663339838788054],
[4.484671994095723, 2.5902066679984634, 16.25695615743613]]
cell = Cell(x)
cell.minkowski_reduce()
