def test_probability_classmethod(self):
file = os.path.join(tests_dir, "cNa3PS4_pda.json")
data = json.load(open(file, "r"))
diff_analyzer = DiffusionAnalyzer.from_dict(data)
#ProbabilityDensityAnalysis object
pda = ProbabilityDensityAnalysis.from_diffusion_analyzer(diffusion_analyzer=diff_analyzer,
interval=0.5)
dV = pda.structure.lattice.volume / pda.lens[0] / pda.lens[1] / pda.lens[2]
Pr_tot = np.sum(pda.Pr) * dV
self.assertAlmostEqual(pda.Pr.max(), 0.0361594977596, 8)
self.assertAlmostEqual(pda.Pr.min(), 0.0, 12)
self.assertAlmostEqual(Pr_tot, 1.0, 12)
def test_probability_classmethod(self):
file = os.path.join(tests_dir, "cNa3PS4_pda.json")
data = json.load(open(file, "r"))
diff_analyzer = DiffusionAnalyzer.from_dict(data)
#ProbabilityDensityAnalysis object
pda = ProbabilityDensityAnalysis.from_diffusion_analyzer(diffusion_analyzer=diff_analyzer,
interval=0.5)
dV = pda.structure.lattice.volume / pda.lens[0] / pda.lens[1] / pda.lens[2]
Pr_tot = np.sum(pda.Pr) * dV
self.assertAlmostEqual(pda.Pr.max(), 0.0361594977596, 8)
self.assertAlmostEqual(pda.Pr.min(), 0.0, 12)
self.assertAlmostEqual(Pr_tot, 1.0, 12)
def test_probability(self):
traj_file = os.path.join(tests_dir, "cNa3PS4_trajectories.npy")
struc_file = os.path.join(tests_dir, "cNa3PS4.cif")
trajectories = np.load(traj_file)
structure = Structure.from_file(struc_file, False)
# ProbabilityDensityAnalysis object
pda = ProbabilityDensityAnalysis(structure, trajectories, interval=0.5)
dV = pda.structure.lattice.volume / pda.lens[0] / pda.lens[1] / pda.lens[2]
Pr_tot = np.sum(pda.Pr) * dV
self.assertAlmostEqual(pda.Pr.max(), 0.030735573102, 12)
self.assertAlmostEqual(pda.Pr.min(), 0.0, 12)
self.assertAlmostEqual(Pr_tot, 1.0, 12)
def test_generate_stable_sites(self):
file = os.path.join(tests_dir, "cNa3PS4_pda.json")
data = json.load(open(file, "r"))
diff_analyzer = DiffusionAnalyzer.from_dict(data)
# ProbabilityDensityAnalysis object
pda = ProbabilityDensityAnalysis.from_diffusion_analyzer(
diffusion_analyzer=diff_analyzer, interval=0.1)
pda.generate_stable_sites(p_ratio=0.25, d_cutoff=1.5)
self.assertEqual(len(pda.stable_sites), 50)
self.assertAlmostEqual(pda.stable_sites[1][2], 0.24113475177304966, 8)
self.assertAlmostEqual(pda.stable_sites[7][1], 0.5193661971830985, 8)
s = pda.get_full_structure()
self.assertEqual(s.num_sites, 178)
self.assertEqual(s.composition["Na"], 48)
self.assertEqual(s.composition["X"], 50)
self.assertAlmostEqual(s[177].frac_coords[2], 0.57446809)