def test_geometry_sort_func_sort():
bi = sisl_geom.bilayer().tile(2, 0).repeat(2, 1)
# Sort according to another cell fractional coordinates
fcc = sisl_geom.fcc(2.4, Atom(6))
def fcc_fracs(axis):
def _(geometry):
return np.dot(geometry.xyz, fcc.icell.T)[:, axis]
return _
out = bi.sort(func_sort=(fcc_fracs(0), fcc_fracs(2)))
def test_geometry_sanitize_atom():
bi = sisl_geom.bilayer(bottom_atoms=Atom[6],
top_atoms=(Atom[5], Atom[7])).tile(2,
0).repeat(2, 1)
C_idx = (bi.atoms.Z == 6).nonzero()[0]
check_C = bi.axyz(C_idx)
only_C = bi.axyz(Atom[6])
assert np.allclose(only_C, check_C)
only_C = bi.axyz(bi.atoms.Z == 6)
assert np.allclose(only_C, check_C)
# with dict redirect
only_C = bi.axyz({'Z': 6})
assert np.allclose(only_C, check_C)
tup_01 = (0, 2)
list_01 = [0, 2]
ndarray_01 = np.array(list_01)
assert np.allclose(bi._sanitize_atoms(tup_01), bi._sanitize_atoms(list_01))
assert np.allclose(bi._sanitize_atoms(ndarray_01),
bi._sanitize_atoms(list_01))
def test_geometry_sort_func():
bi = sisl_geom.bilayer().tile(2, 0).repeat(2, 1)
def reverse(geometry, atom, **kwargs):
return atom[::-1]
atom = [[2, 0], [3, 1]]
out = bi.sort(func=reverse, atom=atom)
all_atoms = np.arange(len(bi))
all_atoms[1] = 2
all_atoms[2] = 1
assert np.allclose(out.xyz, bi.sub(all_atoms).xyz)
# Ensure that they are swapped
atom = [2, 0]
out = bi.sort(func=reverse, atom=atom)
assert np.allclose(out.xyz, bi.xyz)
out = bi.sort(func=reverse)
all_atoms = np.arange(len(bi))[::-1]
assert np.allclose(out.xyz, bi.sub(all_atoms).xyz)
def test_geometry_sort_fail_keyword():
sisl_geom.bilayer().sort(not_found_keyword=True)
def test_geometry_sort_fail_keyword():
with pytest.raises(ValueError):
sisl_geom.bilayer().sort(not_found_keyword=True)