def test_get_local_extrema(self):
ca = ChargeDensityAnalyzer.from_file(self.chgcar_path)
threshold_frac = random.random()
threshold_abs_min = random.randrange(2, 14)
threshold_abs_max = random.randrange(27e2, 28e4)
# Minima test
full_list_min = self.ca_FePO4.get_local_extrema(find_min=True, threshold_frac=1.0)
frac_list_min_frac = self.ca_FePO4.get_local_extrema(find_min=True, threshold_frac=threshold_frac)
frac_list_min_abs = self.ca_FePO4.get_local_extrema(find_min=True, threshold_abs=threshold_abs_min)
self.assertAlmostEqual(len(full_list_min) * threshold_frac, len(frac_list_min_frac), delta=1)
ca.get_local_extrema(find_min=True)
df_expected = ca.extrema_df[ca.extrema_df["Charge Density"] <= threshold_abs_min]
self.assertEqual(len(frac_list_min_abs), len(df_expected))
# Maxima test
full_list_max = self.ca_FePO4.get_local_extrema(find_min=False, threshold_frac=1.0)
frac_list_max = self.ca_FePO4.get_local_extrema(find_min=False, threshold_frac=threshold_frac)
frac_list_max_abs = self.ca_FePO4.get_local_extrema(find_min=False, threshold_abs=threshold_abs_max)
self.assertAlmostEqual(len(full_list_max) * threshold_frac, len(frac_list_max), delta=1)
# Local maxima should finds all center of atoms
self.assertEqual(len(self.ca_FePO4.structure), len(full_list_max))
ca.get_local_extrema(find_min=False)
df_expected = ca.extrema_df[ca.extrema_df["Charge Density"] >= threshold_abs_max]
self.assertEqual(len(frac_list_max_abs), len(df_expected))
def test_sort_sites_by_integrated_chg(self):
print(self.chgcar_path)
ca = ChargeDensityAnalyzer.from_file(self.chgcar_path)
ca.get_local_extrema()
ca.sort_sites_by_integrated_chg()
print(ca._extrema_df.iloc[0], 0.5)
print(ca._extrema_df.iloc[0]["avg_charge_den"])
self.assertAlmostEqual(ca._extrema_df.iloc[0]["a"], 0.0)
self.assertAlmostEqual(ca._extrema_df.iloc[0]["b"], 0.5)
self.assertAlmostEqual(ca._extrema_df.iloc[0]["c"], 0.0)
self.assertAlmostEqual(ca._extrema_df.iloc[0]["Charge Density"], 1.65288944124)
self.assertAlmostEqual(ca._extrema_df.iloc[0]["avg_charge_den"], 0.006831484178753711)
def test_sort_sites_by_integrated_chg(self):
print(self.chgcar_path)
ca = ChargeDensityAnalyzer.from_file(self.chgcar_path)
ca.get_local_extrema()
ca.sort_sites_by_integrated_chg()
print(ca._extrema_df.iloc[0], 0.5)
self.assertAlmostEqual(ca._extrema_df.iloc[0]['a'], 0.0)
self.assertAlmostEqual(ca._extrema_df.iloc[0]['b'], 0.5)
self.assertAlmostEqual(ca._extrema_df.iloc[0]['c'], 0.0)
self.assertAlmostEqual(ca._extrema_df.iloc[0]['Charge Density'],
1.65288944124)
self.assertAlmostEqual(ca._extrema_df.iloc[0]['Int. Charge Density'],
0.0018375161626331743)
def test_sort_sites_by_integrated_chg(self):
print(self.chgcar_path)
ca = ChargeDensityAnalyzer.from_file(self.chgcar_path)
ca.get_local_extrema()
ca.sort_sites_by_integrated_chg()
print(ca._extrema_df.iloc[0], 0.5)
print(ca._extrema_df.iloc[0]['avg_charge_den'])
self.assertAlmostEqual(ca._extrema_df.iloc[0]['a'], 0.0)
self.assertAlmostEqual(ca._extrema_df.iloc[0]['b'], 0.5)
self.assertAlmostEqual(ca._extrema_df.iloc[0]['c'], 0.0)
self.assertAlmostEqual(ca._extrema_df.iloc[0]['Charge Density'],
1.65288944124)
self.assertAlmostEqual(ca._extrema_df.iloc[0]['avg_charge_den'],
0.006831484178753711)
def test_from_file(self):
ca = ChargeDensityAnalyzer.from_file(self.chgcar_path)
self.assertTrue(isinstance(ca, ChargeDensityAnalyzer))
def test_from_file(self):
ca = ChargeDensityAnalyzer.from_file(self.chgcar_path)
self.assertTrue(isinstance(ca, ChargeDensityAnalyzer))