def test_neighbors():
atom = pc.Atom(pos=[0, 0, 0], id=1)
atom.neighbors = [1, 2]
assert atom.neighbors == [1, 2]
assert atom.coordination == 2
atom.neighbor_weights = [0.6, 0.4]
assert atom.neighbor_weights == [0.6, 0.4]
def _get_steinhardt_parameter(cell, positions, cutoff=3.50, n_clusters=2, q=[4, 6]):
sys = pc.System()
prism = UnfoldingPrism(cell, digits=15)
xhi, yhi, zhi, xy, xz, yz = prism.get_lammps_prism_str()
coords = [prism.pos_to_lammps(position) for position in positions]
sys.box = [[0.0, float(xhi)], [0.0, float(yhi)], [0.0, float(zhi)]]
sys.atoms = [pc.Atom(pos=p, id=i) for i, p in enumerate(coords)]
sys.find_neighbors(method='cutoff', cutoff=cutoff)
sys.calculate_q(q, averaged=True)
sysq = sys.get_qvals(q, averaged=True)
cl = cluster.KMeans(n_clusters=n_clusters)
ind = cl.fit(list(zip(*sysq))).labels_ == 0
return sysq, ind
def test_set_solid():
atom = pc.Atom(pos=[0, 0, 0], id=1, type=1)
atom.solid = 1
assert atom.solid == 1
with pytest.raises(ValueError):
atom.solid = 2
def test_set_type():
atom = pc.Atom(pos=[0, 0, 0], id=1, type=1)
assert atom.type == 1
atom.type = 2
assert atom.type == 2
def test_set_x():
atom = pc.Atom(pos=[0, 0, 0], id=1)
newx = [0, 0, 2]
atom.pos = newx
assert atom.pos == newx
def test_get_x():
atom = pc.Atom(pos=[0, 0, 0], id=1)
assert atom.pos == [0, 0, 0]
atom.id = 5
assert atom.id == 5
def test_set_solid():
atom = pc.Atom(pos=[0, 0, 0], id=1, type=1)
atom.solid = 1
assert atom.solid == 1
