def test_get_df(self):
data_file = os.path.join(tests_dir, "cNa3PS4_pda.json")
data = json.load(open(data_file, "r"))
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
eva = EvolutionAnalyzer(structure_list, rmax=10, step=1, time_step=2)
rdf = eva.get_df(EvolutionAnalyzer.rdf, pair=("Na", "Na"))
atom_dist = eva.get_df(EvolutionAnalyzer.atom_dist, specie="Na", direction="c")
check = np.shape(rdf) == (10, 101) and np.shape(atom_dist) == (10, 101) and eva.pairs[0] == ("Na", "Na")
self.assertTrue(check)
self.assertAlmostEqual(max(np.array(rdf)[0]), 1.82363640047, 4)
def test_get_df(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
eva = EvolutionAnalyzer(structure_list, rmax=10, step=1, time_step=2)
rdf = eva.get_df(EvolutionAnalyzer.rdf, pair=("Na", "Na"))
atom_dist = eva.get_df(EvolutionAnalyzer.atom_dist, specie="Na",
direction="c")
check = np.shape(rdf) == (10, 101) and np.shape(atom_dist) == (
10, 101) and ("Na", "Na") in eva.pairs
self.assertTrue(check)
self.assertAlmostEqual(max(np.array(rdf)[0]), 1.772465, 4)
import os
from pymatgen.io.vasp import Xdatcar
from pymatgen_diffusion.aimd.van_hove import EvolutionAnalyzer
os.chdir('/home/jinho93/oxides/cluster/zno/vasp/1.aimd/2.10A/2.02/3fs')
structures = Xdatcar('XDATCAR').structures
e = EvolutionAnalyzer(structures)
for s in structures:
s.substitute()
e.plot_rdf_evolution(('O', 'O'))