# Copyright (c) Materials Virtual Lab.
# Distributed under the terms of the BSD License.
from __future__ import annotations
__author__ = "Iek-Heng Chu"
__date__ = "01/16"
import json
import os
import unittest
import numpy as np
from pymatgen.analysis.diffusion.aimd.pathway import ProbabilityDensityAnalysis, SiteOccupancyAnalyzer
from pymatgen.analysis.diffusion.analyzer import DiffusionAnalyzer
from pymatgen.core import Structure
from pymatgen.io.vasp import Chgcar
tests_dir = os.path.dirname(os.path.abspath(__file__))
[docs]
class ProbabilityDensityTest(unittest.TestCase):
[docs]
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)
[docs]
def test_probability_classmethod(self):
file = os.path.join(tests_dir, "cNa3PS4_pda.json")
data = json.load(open(file))
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)
[docs]
def test_generate_stable_sites(self):
file = os.path.join(tests_dir, "cNa3PS4_pda.json")
data = json.load(open(file))
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)
assert 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()
assert s.num_sites == 178
assert s.composition["Na"] == 48
assert s.composition["X"] == 50
self.assertAlmostEqual(s[177].frac_coords[2], 0.57446809)
[docs]
def test_to_chgcar(self):
file = os.path.join(tests_dir, "cNa3PS4_pda.json")
data = json.load(open(file))
diff_analyzer = DiffusionAnalyzer.from_dict(data)
# ProbabilityDensityAnalysis object
pda = ProbabilityDensityAnalysis.from_diffusion_analyzer(diffusion_analyzer=diff_analyzer, interval=0.1)
pda.to_chgcar("CHGCAR.PDA")
chgcar = Chgcar.from_file("CHGCAR.PDA")
assert pda.structure.species == chgcar.structure.species
os.remove("CHGCAR.PDA")
[docs]
class SiteOccupancyTest(unittest.TestCase):
[docs]
def test_site_occupancy(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)
coords_ref = [ss.frac_coords for ss in structure if ss.specie.symbol == "Na"]
# SiteOccupancyAnalyzer object
socc = SiteOccupancyAnalyzer(structure, coords_ref, trajectories, species=("Li", "Na"))
site_occ = socc.site_occ
self.assertAlmostEqual(np.sum(site_occ), len(coords_ref), 12)
self.assertAlmostEqual(site_occ[11], 0.98, 12)
self.assertAlmostEqual(site_occ[15], 0.875, 12)
assert len(coords_ref) == 48
[docs]
def test_site_occupancy_classmethod(self):
file = os.path.join(tests_dir, "cNa3PS4_pda.json")
data = json.load(open(file))
diff_analyzer = DiffusionAnalyzer.from_dict(data)
structure = diff_analyzer.structure
coords_ref = [ss.frac_coords for ss in structure if ss.specie.symbol == "Na"]
# SiteOccupancyAnalyzer object
socc = SiteOccupancyAnalyzer.from_diffusion_analyzer(coords_ref, diffusion_analyzer=diff_analyzer)
site_occ = socc.site_occ
self.assertAlmostEqual(np.sum(site_occ), len(coords_ref), 12)
self.assertAlmostEqual(site_occ[1], 0.98, 12)
self.assertAlmostEqual(site_occ[26], 0.97, 12)
assert len(coords_ref) == 48