def test_equal(self):
s1 = Site((1, 2, 0), 'S')
s2 = Site((1, 2, 0), Specie('S'))
s3 = Site((1, 2, 0), 16)
self.assertEqual(s1, s1)
self.assertEqual(s1, s2)
self.assertEqual(s1, s3)
def test_append_sites(self):
l_sites = [Site((0, 0, k), 'S') for k in [0.1, 0.2, 0.3]]
initstru = self.initstru.copy()
new_stru = initstru.append_sites(l_sites)
gcell = new_stru.to_gcell()
new_pos = np.array([[0, 0, 0], [0, 0, 0.1], [0, 0, 0.2], [0, 0, 0.3]])
self.assertTrue(np.array_equal(gcell.positions, new_pos))
def __init__(self,
lattice,
positions=np.array([[0, 0, 0]]),
numbers=np.array([0])):
self._lattice = lattice
lsites = [s for s in zip(positions.tolist(), numbers.tolist())]
self._sites = [Site(s[0], s[1]) for s in lsites]
def test_append_site(self):
site_s = Site((0, 0, 0.222), 'S')
initstru = self.initstru.copy()
new_stru = initstru.append_site(site_s)
gcell = new_stru.to_gcell()
new_pos = np.append([[0, 0, 0]], [[0, 0, 0.222]], axis=0)
self.assertTrue(new_stru is initstru)
self.assertTrue(np.array_equal(gcell.positions, new_pos))
def test_append(self):
site_s = Site((0, 0, 0.222), 'S')
zb = self.full_initzb.copy()
zb.append(site_s)
gcell = zb.to_gcell()
new_pos = np.insert(self.pos, 1, [[0, 0, 0.222]], axis=0)
new_numbers = np.insert(self.numbers, 1, 16)
self.assertTrue(np.array_equal(gcell.positions, new_pos))
self.assertTrue(np.array_equal(gcell.numbers, new_numbers))
def test_get_points_in_sphere(self):
latt = np.array([[4.898979, 0.000000, 0.000000],
[2.449490, 4.242641, 0.000000],
[1.632993, -0.000000, 4.618802]])
pos = np.array([[0.208333, 0.333333, 0.375000],
[0.375000, 0.000000, 0.875000],
[0.541667, 0.666667, 0.375000],
[0.708333, 0.333333, 0.875000],
[0.875000, 0.000000, 0.375000],
[0.000000, 0.000000, 0.000000],
[0.166667, 0.666667, 0.500000],
[0.333333, 0.333333, 0.000000],
[0.500000, 0.000000, 0.500000],
[0.666667, 0.666667, 0.000000],
[0.833333, 0.333333, 0.500000],
[0.041667, 0.666667, 0.875000]])
numbers = np.array([16, 16, 16, 16, 16, 30, 30, 30, 30, 30, 30, 55])
modcell = ModifiedCell(latt, pos, numbers)
dict_sites = modcell.get_points_incell_insphere(
np.array([0.041667, 0.666667, 0.875000]), 2)
sites = [
Site(pos[5], 'Zn'),
Site(pos[9], 'Zn'),
Site(pos[7], 'Zn'),
Site(pos[6], 'Zn'),
Site(pos[11], 'Cs')
]
self.assertEqual(len(dict_sites), 5)
for s in dict_sites.values():
self.assertTrue(s in sites)
# Test for find giving element
modcell = ModifiedCell(latt, pos, numbers)
dict_sites = modcell.get_points_incell_insphere(
np.array([0.041667, 0.666667, 0.875000]), 2, Specie('Zn'))
sites = [
Site(pos[5], 'Zn'),
Site(pos[9], 'Zn'),
Site(pos[7], 'Zn'),
Site(pos[6], 'Zn')
]
self.assertEqual(len(dict_sites), 4)
for s in dict_sites.values():
self.assertTrue(s in sites)
def test_init(self):
s = Site((1, 2, 0), 'S')
s = Site((1, 2, 0), Specie('S'))
s = Site((1, 2, 0), 16)