def test_rdf_coordination_number(self):
# create a simple cubic lattice
coords = np.array([[0.5, 0.5, 0.5]])
atom_list = ['S']
lattice = Lattice.from_parameters(a=1.0, b=1.0, c=1.0, alpha=90,
beta=90, gamma=90)
structure = Structure(lattice, atom_list, coords)
rdf = RadialDistributionFunction.from_species(
structures=[structure], species=['S'],
rmax=5.0, sigma=0.1, ngrid=500)
self.assertEqual(rdf.coordination_number[100], 6.0)
def test_rdf(self):
# Parse the DiffusionAnalyzer object from json file directly
obj = loadfn(os.path.join(tests_dir, "cNa3PS4_pda.json"))
structure_list = []
for i, s in enumerate(obj.get_drift_corrected_structures()):
structure_list.append(s)
if i == 9: break
species = ["Na", "P", "S"]
# Test from_species
obj = RadialDistributionFunction.from_species(
structures=structure_list, ngrid=101, rmax=10.0, cell_range=1,
sigma=0.1, species=species, reference_species=species)
check = np.shape(obj.rdf)[0] == 101 and np.argmax(obj.rdf) == 34
self.assertTrue(check)
self.assertAlmostEqual(obj.rdf.max(), 1.634448, 4)
# Test init
s = structure_list[0]
indices = [i for (i, site) in enumerate(s) if
site.species_string in species]
obj = RadialDistributionFunction(
structures=structure_list, ngrid=101, rmax=10.0, cell_range=1,
sigma=0.1, indices=indices, reference_indices=indices)
check = np.shape(obj.rdf)[0] == 101 and np.argmax(obj.rdf) == 34
self.assertTrue(check)
self.assertAlmostEqual(obj.rdf.max(), 1.634448, 4)
# Test init using structures w/ different lattices
s0 = deepcopy(structure_list[0])
sl_1 = [s0, s0, s0 * [1, 2, 1]]
sl_2 = [s0 * [2, 1, 1], s0, s0]
obj_1 = RadialDistributionFunction(
structures=sl_1, ngrid=101, rmax=10.0, cell_range=1,
sigma=0.1, indices=indices, reference_indices=indices)
obj_2 = RadialDistributionFunction(
structures=sl_2, ngrid=101, rmax=10.0, cell_range=1,
sigma=0.1, indices=indices, reference_indices=indices)
self.assertEqual(obj_1.rho, obj_2.rho)
self.assertEqual(obj_1.rdf[0], obj_2.rdf[0])
def test_rdf(self):
data_file = os.path.join(tests_dir, "cNa3PS4_pda.json")
with open(data_file, "r") as j:
data = json.load(j)
obj = DiffusionAnalyzer.from_dict(data)
structure_list = []
for i, s in enumerate(obj.get_drift_corrected_structures()):
structure_list.append(s)
if i == 9: break
species = ["Na", "P", "S"]
# Test from_species
obj = RadialDistributionFunction.from_species(
structures=structure_list,
ngrid=101,
rmax=10.0,
cell_range=1,
sigma=0.1,
species=species,
reference_species=species)
check = np.shape(obj.rdf)[0] == 101 and np.argmax(obj.rdf) == 34
self.assertTrue(check)
self.assertAlmostEqual(obj.rdf.max(), 1.634448, 4)
# Test init
s = structure_list[0]
indices = [
i for (i, site) in enumerate(s) if site.species_string in species
]
obj = RadialDistributionFunction(structures=structure_list,
ngrid=101,
rmax=10.0,
cell_range=1,
sigma=0.1,
indices=indices,
reference_indices=indices)
check = np.shape(obj.rdf)[0] == 101 and np.argmax(obj.rdf) == 34
self.assertTrue(check)
self.assertAlmostEqual(obj.rdf.max(), 1.634448, 4)
def test_rdf_two_species_coordination_number(self):
# create a structure with interpenetrating simple cubic lattice
coords = np.array([[0.0, 0.0, 0.0], [0.5, 0.5, 0.5]])
atom_list = ["S", "Zn"]
lattice = Lattice.from_parameters(a=1.0,
b=1.0,
c=1.0,
alpha=90,
beta=90,
gamma=90)
structure = Structure(lattice, atom_list, coords)
rdf = RadialDistributionFunction.from_species(
structures=[structure],
species=["S"],
reference_species=["Zn"],
rmax=5.0,
sigma=0.1,
ngrid=500,
)
self.assertEqual(rdf.coordination_number[100], 8.0)
def test_raises_ValueError_if_reference_species_not_in_structure(self):
with self.assertRaises(ValueError):
rdf = RadialDistributionFunction.from_species(
structures=[self.structure],
species=['S'],
reference_species=['Cl'])
def test_raises_ValueError_if_sigma_is_not_positive(self):
with self.assertRaises(ValueError):
rdf = RadialDistributionFunction.from_species(
structures=[self.structure], sigma=0)
def test_raises_valueerror_if_ngrid_is_less_than_2(self):
with self.assertRaises(ValueError):
rdf = RadialDistributionFunction.from_species(
structures=[self.structure], ngrid=1)