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import pytest
import numpy as np
from numpy.testing import assert_allclose, assert_almost_equal
from ase.geometry import minkowski_reduce
from ase.cell import Cell
TOL = 1E-14
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()
def test_cycle():
# Without cycle-checking in the MR code, this cell causes failure
a, b, c = 4.374006080444519, 2.0714140579127145, 3.671070851026261
cell = np.array([[-a, b, c], [a, c, b], [a, b, c]])
minkowski_reduce(cell)
@pytest.mark.parametrize("it", range(10))
def test_random(it):
rng = np.random.RandomState(seed=it)
B = rng.uniform(-1, 1, (3, 3))
R, H = minkowski_reduce(B)
assert_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(int)).all()
rcell, _ = Cell(B).minkowski_reduce()
assert_allclose(rcell, R, atol=TOL)
class TestKnownUnimodularMatrix():
def setup_method(self):
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_almost_equal(np.linalg.det(unimodular), 1)
self.lcell = unimodular.T @ cell
@pytest.mark.parametrize("pbc", [1, True, (1, 1, 1)])
def test_pbc(self, pbc):
lcell = self.lcell
rcell, op = minkowski_reduce(lcell, pbc=pbc)
assert_almost_equal(np.linalg.det(rcell), 1)
rdet = np.linalg.det(rcell)
ldet = np.linalg.det(lcell)
assert np.sign(ldet) == np.sign(rdet)
def test_0d(self):
lcell = self.lcell
rcell, op = minkowski_reduce(lcell, pbc=[0, 0, 0])
assert (rcell == lcell).all() # 0D reduction does nothing
@pytest.mark.parametrize("axis", range(3))
def test_1d(self, axis):
lcell = self.lcell
rcell, op = minkowski_reduce(lcell, pbc=np.roll([1, 0, 0], axis))
assert (rcell == lcell).all() # 1D reduction does nothing
zcell = np.zeros((3, 3))
zcell[0] = lcell[0]
rcell, _ = Cell(zcell).minkowski_reduce()
assert_allclose(rcell, zcell, atol=TOL)
@pytest.mark.parametrize("axis", range(3))
def test_2d(self, axis):
lcell = self.lcell
pbc = np.roll([0, 1, 1], axis)
rcell, op = minkowski_reduce(lcell.astype(float), pbc=pbc)
assert (rcell[axis] == lcell[axis]).all()
zcell = np.copy(lcell)
zcell[axis] = 0
rzcell, _ = Cell(zcell).minkowski_reduce()
rcell[axis] = 0
assert_allclose(rzcell, rcell, atol=TOL)
def test_3d(self):
lcell = self.lcell
rcell, op = minkowski_reduce(lcell)
assert_almost_equal(np.linalg.det(rcell), 1)
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