def test_substrate(self):
# Tests `substrate` and `set_substrate` methods
h = sc.heterostructure()
sub = sc.lattice()
h.set_substrate(sub)
self.assertEqual(h.substrate(), sub)
h = sc.heterostructure()
with self.assertRaises(AttributeError):
h.substrate()
def test_opt(self, algorithm="fast"):
# graphene-NiPS3 low-strain angle 21.9, theta range 16-30-0.1
graphene = sc.read_POSCAR(path.join(
path.dirname(__file__), "../resources/vasp/graphene/POSCAR"),
atomic_species=["C"])
nips3 = sc.read_POSCAR(path.join(path.dirname(__file__),
"../resources/vasp/NiPS3/POSCAR"),
atomic_species=["Ni", "P", "S"])
h = sc.heterostructure()
h.set_substrate(graphene)
h.add_layer(nips3)
res = h.opt(max_el=11,
thetas=np.arange(16 * sc.DEGREE, 30 * sc.DEGREE,
0.1 * sc.DEGREE),
algorithm=algorithm)
self.assertTrue(
np.allclose(res.M(), np.array([[7, 9], [10, -8]]))
or np.allclose(res.M(), np.array([[9, 7], [-8, 10]])))
self.assertTrue(
np.allclose(res.layer_Ms()[0], np.array([[6, -1], [-1, -2]]))
or np.allclose(res.layer_Ms()[0], np.array([[-1, 6], [-2, -1]])))
self.assertAlmostEqual(res.thetas()[0], 21.9 * sc.DEGREE)
self.assertAlmostEqual(res.max_strain(), 0.000608879275296, places=5)
self.assertEqual(res.atom_count(), 552)
def test_bad_arg_thetas(self):
graphene = sc.read_POSCAR(path.join(
path.dirname(__file__), "../resources/vasp/graphene/POSCAR"),
atomic_species=["C"])
h = sc.heterostructure().set_substrate(graphene).add_layer(
graphene).add_layer(graphene)
with self.assertRaises(TypeError):
h.opt(max_el=4,
thetas=[np.arange(0, 10 * sc.DEGREE, 1 * sc.DEGREE)])
def test_homogeneous_trilayer(self):
graphene = sc.read_POSCAR(path.join(
path.dirname(__file__), "../resources/vasp/graphene/POSCAR"),
atomic_species=["C"])
h = sc.heterostructure().set_substrate(graphene).add_layer(
graphene).add_layer(graphene)
res = h.opt(max_el=4,
thetas=[np.arange(0, 10 * sc.DEGREE, 1 * sc.DEGREE)] * 2)
self.assertEqual(res.atom_count(), 3 * len(graphene.atoms()))
def test_layers(self):
# Tests `layers`, `add_layer`, `add_layers`, `remove_layer`,
# and `get_layer` methods
h = sc.heterostructure()
lay = sc.lattice()
lay.add_atom("H", (0, 0, 0))
h.add_layer(lay, theta=1 * sc.DEGREE)
lay2 = sc.lattice()
lay2.add_atom("He", (0.1, 0.1, 0.1))
h.add_layer(lay2)
lay3 = sc.lattice()
lay3.add_atom("Li", (0.2, 0.2, 0.2))
h.add_layer(lay3, theta=(0, 45 * sc.DEGREE, 0.2 * sc.DEGREE))
lay4 = sc.lattice()
lay4.add_atom("Be", (0.3, 0.3, 0.3))
h.add_layer(lay4, pos=1)
self.assertEqual([lay, lay4, lay2, lay3], h.layers())
h.remove_layer(1)
self.assertEqual([lay, lay2, lay3], h.layers())
h = sc.heterostructure()
h.add_layers([(lay, 1 * sc.DEGREE), lay2,
(lay3, (0, 45 * sc.DEGREE, 0.2 * sc.DEGREE)), lay4])
self.assertEqual([lay, lay2, lay3, lay4], h.layers())
got_lay = h.get_layer(0)
self.assertEqual(lay, got_lay[0])
self.assertEqual((1 * sc.DEGREE, 1 * sc.DEGREE, 1.0), got_lay[1])
with self.assertRaises(IndexError):
h.get_layer(10)
def test_opt_graphene_fast(self):
graphene = sc.read_POSCAR(path.join(
path.dirname(__file__), "../resources/vasp/graphene/POSCAR"),
atomic_species=["C"])
h = sc.heterostructure()
h.set_substrate(graphene)
h.add_layer(graphene)
res = h.opt(max_el=20,
thetas=np.arange(5.5 * sc.DEGREE, 7 * sc.DEGREE,
0.001 * sc.DEGREE))
self.assertAlmostEqual(res.max_strain(), 0, places=6)
self.assertEqual(res.atom_count(), 364)
import supercell_core as sc
# Read graphene and NiPS3 definition from POSCAR
graphene = sc.read_POSCAR("supercell_core/resources/vasp/POSCAR_Gr")
nips3 = sc.read_POSCAR("supercell_core/resources/vasp/POSCAR_NiPS3")
h = sc.heterostructure().set_substrate(graphene)\
.add_layer(nips3)
res = h.opt(max_el=8, thetas=[np.arange(0, 30 * sc.DEGREE, 0.25 * sc.DEGREE)])
# Draw the resulting supercell
res.superlattice().draw()
plt.title("""Best supercell found for $\\theta$ =
{} max strain = {:.4g}""".format(res.thetas()[0], res.max_strain()))
