def test_raise_warning(self):
with warnings.catch_warnings(record=True) as w:
xanes_test = XANES(self.test_row_x,
self.test_row_spect,
self.test_row_absorb_specie,
edge="K",
**self.test_row_add_paras)
self.assertTrue("maximum derivative" in str(w[-1].message))
self.assertEqual(xanes_test.composition, "NaB(CO2)4")
self.assertEqual(len(xanes_test.x), 200)
self.assertEqual(xanes_test.xas_id, "mp-559618-4-XANES-K")
self.assertEqual(xanes_test.elemental_group, "Carbon")
with warnings.catch_warnings(record=True) as w:
xanes_test_2 = XANES(
self.test_row_x,
self.test_row_spect,
self.test_row_absorb_specie,
edge="K",
e0=self.test_row_energy_e0,
**self.test_row_add_paras,
)
self.assertEqual(len(w), 0)
self.assertEqual(xanes_test_2.composition, "NaB(CO2)4")
self.assertEqual(len(xanes_test_2.x), 200)
self.assertEqual(xanes_test_2.e0, 274.98)
self.assertEqual(xanes_test_2.xas_id, "mp-559618-4-XANES-K")
self.assertEqual(xanes_test_2.elemental_group, "Carbon")
def setUp(self):
self.test_row = comp_test_df.iloc[0]
self.test_row_formula = self.test_row["formula"]
self.test_row_ele_group = self.test_row["ele_tm_alka_metalloid"]
self.test_row_xas_id = self.test_row["xas_id"]
self.test_row_absorb_specie = self.test_row["absorbing_species"]
self.test_row_energy_e0 = self.test_row["energy_e0"]
self.test_row_structure = self.test_row["structure"]
self.test_row_x = self.test_row["x_axis_energy_55eV"]
self.test_row_spect = self.test_row["interp_spectrum_55eV"]
self.test_row_x_45 = self.test_row["x_axis_energy_45eV"]
self.test_row_spect_45 = self.test_row["interp_spectrum_45eV"]
self.test_row_add_paras = {
"composition": self.test_row_formula,
"elemental_group": self.test_row_ele_group,
"xas_id": self.test_row_xas_id,
"energy_45eV": self.test_row_x_45,
"spectrum_45eV": self.test_row_spect_45,
}
self.xanes_obj = XANES(
self.test_row_x,
self.test_row_spect,
self.test_row_absorb_specie,
edge="K",
e0=self.test_row_energy_e0,
**self.test_row_add_paras,
)
def test_cenv_prediction_cnn(self):
self.Al2O3_origin_obj = XANES(
Al2O3_dataset["prev_interp_energy"],
Al2O3_dataset["prev_interp_spectrum"],
Al2O3_dataset["absorbing_species"],
edge="K",
e0=Al2O3_dataset["edge_energy"],
)
self.Al2O3_cenv_pred_origin = CenvPrediction(
self.Al2O3_origin_obj,
"E0",
energy_range=Al2O3_dataset["energy_range"],
edge_energy=Al2O3_dataset["edge_energy"],
spectrum_interpolation=False,
model_dir=model_dir,
extra_model_dir=model_dir,
model="cnn",
)
self.Al2O3_cenv_pred_origin.cenv_prediction()
self.assertEqual(self.Al2O3_cenv_pred_origin.pred_cnum_ranklist,
"CN_4-CN_3-CN_6")
self.assertEqual(
self.Al2O3_cenv_pred_origin.pred_cenv[0],
"CN_4-tetrahedral-trigonal pyramidal-see-saw-like-square co-planar",
)
def test_tsv_loading(self):
self.Fe_xanes = XANES.from_K_XANES_MP_tsv(Fe_tsv, sep='\t', header=3)
self.Fe_CenvPred = CenvPrediction(self.Fe_xanes, 'lowest', 45)
self.Fe_CenvPred.cenv_prediction()
self.assertEqual(self.Fe_CenvPred.pred_cnum_ranklist, 'CN_4')
self.assertEqual(self.Fe_CenvPred.pred_cenv[0],
'CN_4-tetrahedral-trigonal pyramidal-see-saw-like-square co-planar')
def test_cenv_prediction(self):
self.Al2O3_origin_obj = XANES(Al2O3_dataset['prev_interp_energy'], Al2O3_dataset['prev_interp_spectrum'],
Al2O3_dataset['absorbing_species'], edge='K', e0=Al2O3_dataset['edge_energy'])
self.Al2O3_cenv_pred_origin = CenvPrediction(self.Al2O3_origin_obj, 'E0',
energy_range=Al2O3_dataset['energy_range'],
edge_energy=Al2O3_dataset['edge_energy'],
spectrum_interpolation=False,
model_dir=model_dir)
self.Al2O3_cenv_pred_origin.cenv_prediction()
self.assertEqual(self.Al2O3_cenv_pred_origin.pred_cnum_ranklist, 'CN_6')
self.assertEqual(self.Al2O3_cenv_pred_origin.pred_cenv[0], 'CN_6 coord. motif undetermined')
def test_cenv_prediction_cnn(self):
self.Al2O3_origin_obj = XANES(Al2O3_dataset['prev_interp_energy'], Al2O3_dataset['prev_interp_spectrum'],
Al2O3_dataset['absorbing_species'], edge='K', e0=Al2O3_dataset['edge_energy'])
self.Al2O3_cenv_pred_origin = CenvPrediction(self.Al2O3_origin_obj, 'E0',
energy_range=Al2O3_dataset['energy_range'],
edge_energy=Al2O3_dataset['edge_energy'],
spectrum_interpolation=False,
model_dir=model_dir,
extra_model_dir=model_dir,
model='cnn')
self.Al2O3_cenv_pred_origin.cenv_prediction()
self.assertEqual(self.Al2O3_cenv_pred_origin.pred_cnum_ranklist, 'CN_4-CN_3-CN_6')
self.assertEqual(self.Al2O3_cenv_pred_origin.pred_cenv[0],
'CN_4-tetrahedral-trigonal pyramidal-see-saw-like-square co-planar')
def setUp(self):
self.test_row = comp_test_df.iloc[0]
self.test_row_formula = self.test_row['formula']
self.test_row_ele_group = self.test_row['ele_tm_alka_metalloid']
self.test_row_xas_id = self.test_row['xas_id']
self.test_row_absorb_specie = self.test_row['absorbing_species']
self.test_row_energy_e0 = self.test_row['energy_e0']
self.test_row_structure = self.test_row['structure']
self.test_row_x = self.test_row['x_axis_energy_55eV']
self.test_row_spect = self.test_row['interp_spectrum_55eV']
self.test_row_x_45 = self.test_row['x_axis_energy_45eV']
self.test_row_spect_45 = self.test_row['interp_spectrum_45eV']
self.test_row_add_paras = {
'composition': self.test_row_formula, 'elemental_group': self.test_row_ele_group,
'xas_id': self.test_row_xas_id, 'energy_45eV': self.test_row_x_45,
'spectrum_45eV': self.test_row_spect_45
}
self.xanes_obj = XANES(self.test_row_x, self.test_row_spect, self.test_row_absorb_specie,
edge='K', e0=self.test_row_energy_e0, **self.test_row_add_paras)
def test_cenv_prediction(self):
self.Al2O3_origin_obj = XANES(
Al2O3_dataset["prev_interp_energy"],
Al2O3_dataset["prev_interp_spectrum"],
Al2O3_dataset["absorbing_species"],
edge="K",
e0=Al2O3_dataset["edge_energy"],
)
self.Al2O3_cenv_pred_origin = CenvPrediction(
self.Al2O3_origin_obj,
"E0",
energy_range=Al2O3_dataset["energy_range"],
edge_energy=Al2O3_dataset["edge_energy"],
spectrum_interpolation=False,
model_dir=model_dir,
)
self.Al2O3_cenv_pred_origin.cenv_prediction()
self.assertEqual(self.Al2O3_cenv_pred_origin.pred_cnum_ranklist,
"CN_6")
self.assertEqual(self.Al2O3_cenv_pred_origin.pred_cenv[0],
"CN_6 coord. motif undetermined")