def feff_task_to_spectrum(doc):
energy = doc["spectrum"][0] # (eV)
intensity = doc["spectrum"][3] # (mu)
structure: Structure = Structure.from_dict(doc["structure"])
# Clean site properties
for site_prop in structure.site_properties.keys():
structure.remove_site_property(site_prop)
absorbing_index = doc["absorbing_atom"]
absorbing_element = structure[absorbing_index].specie
edge = doc["edge"]
spectrum_type = doc["spectrum_type"]
spectrum = XAS(
x=energy,
y=intensity,
structure=structure,
absorbing_element=absorbing_element,
absorbing_index=absorbing_index,
edge=edge,
spectrum_type=spectrum_type,
)
# Adding a attr is not a robust process
# Figure out better solution later
spectrum.last_updated = doc["last_updated"]
spectrum.task_ids = [doc["xas_id"]]
return spectrum
def test_stitch_l23(self):
self.l2_xanes.y[0] = 0.1
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter("always")
XAS.stitch(self.l2_xanes, self.l3_xanes, 100, mode="L23")
self.assertEqual(len(w), 1)
self.assertIs(w[-1].category, UserWarning)
self.assertIn("jump", str(w[-1].message))
self.l2_xanes = XAS.from_dict(l2_xanes_dict)
l23 = XAS.stitch(self.l2_xanes, self.l3_xanes, 100, mode="L23")
self.assertIsInstance(l23, XAS)
self.assertEqual("L23", l23.edge)
self.assertAlmostEqual(min(l23.x), min(self.l3_xanes.x), 3)
self.assertAlmostEqual(max(l23.x), max(self.l3_xanes.x), 3)
self.assertTrue(np.greater_equal(l23.y, self.l2_xanes.y).all())
self.assertEqual(len(l23.x), 100)
self.l2_xanes.spectrum_type = "EXAFS"
self.assertRaises(ValueError,
XAS.stitch,
self.l2_xanes,
self.l3_xanes,
mode="L23")
self.l2_xanes.absorbing_element = Element("Pt")
self.assertRaises(ValueError,
XAS.stitch,
self.l2_xanes,
self.l3_xanes,
mode="L23")
self.assertRaises(ValueError,
XAS.stitch,
self.k_xanes,
self.l3_xanes,
mode="L23")
def setUp(self):
self.Al2O3_xane_1 = XAS(Al2O3_spect['x'], Al2O3_spect['y'], Al2O3_stru, Element('Al'), 'K')
self.Al2O3_xane_2 = deepcopy(self.Al2O3_xane_1)
self.Al2O3_xane_2.x = self.Al2O3_xane_2.x - 40
self.Al2O3_xane_left_shift5 = deepcopy(self.Al2O3_xane_1)
self.Al2O3_xane_left_shift5.x = self.Al2O3_xane_left_shift5.x - 5
self.Al2O3_xane_right_shift5 = deepcopy(self.Al2O3_xane_1)
self.Al2O3_xane_right_shift5.x = self.Al2O3_xane_right_shift5.x + 5
self.LiCoO2_xane = XAS(LiCoO2_spect['x'], LiCoO2_spect['y'], LiCoO2_stru, Element('Co'), 'K')
def test_stitch_xafs(self):
self.assertRaises(ValueError,
XAS.stitch,
self.k_xanes,
self.k_exafs,
mode="invalid")
xafs = XAS.stitch(self.k_xanes, self.k_exafs, mode="XAFS")
self.assertIsInstance(xafs, XAS)
self.assertEqual("XAFS", xafs.spectrum_type)
self.assertEqual(len(xafs.x), 500)
self.assertAlmostEqual(min(xafs.x), min(self.k_xanes.x), 2)
self.assertAlmostEqual(max(xafs.y), max(self.k_xanes.y), 2)
self.assertAlmostEqual(
xafs.x[np.argmax(np.gradient(xafs.y) / np.gradient(xafs.x))],
self.k_xanes.e0,
2,
)
self.assertRaises(ValueError,
XAS.stitch,
self.k_xanes,
self.l2_xanes,
mode="XAFS")
self.k_xanes.x = np.zeros(100)
self.assertRaises(ValueError, XAS.stitch, self.k_xanes, self.k_exafs)
self.k_xanes.absorbing_element = Element("Pt")
self.assertRaises(ValueError,
XAS.stitch,
self.k_xanes,
self.k_exafs,
mode="XAFS")
def test_stitch_l23(self):
l23 = XAS.stitch(self.l2_xanes, self.l3_xanes, 100, mode="L23")
self.assertIsInstance(l23, XAS)
self.assertEqual("L23", l23.edge)
self.assertAlmostEqual(min(l23.x), min(self.l3_xanes.x), 3)
self.assertAlmostEqual(max(l23.x), max(self.l2_xanes.x), 3)
self.assertTrue(np.greater_equal(l23.y, self.l2_xanes.y).all())
self.assertEqual(len(l23.x), 100)
self.l2_xanes.spectrum_type = "EXAFS"
self.assertRaises(ValueError,
XAS.stitch,
self.l2_xanes,
self.l3_xanes,
mode="L23")
self.l2_xanes.absorbing_element = Element("Pt")
self.assertRaises(ValueError,
XAS.stitch,
self.l2_xanes,
self.l3_xanes,
mode="L23")
self.assertRaises(ValueError,
XAS.stitch,
self.k_xanes,
self.l3_xanes,
mode="L23")
def setUp(self):
self.k_xanes = XAS.from_dict(k_xanes_dict)
self.k_exafs = XAS.from_dict(k_exafs_dict)
self.l2_xanes = XAS.from_dict(l2_xanes_dict)
self.l3_xanes = XAS.from_dict(l3_xanes_dict)
self.site1_xanes = XAS.from_dict(site1_xanes_dict)
self.site2_xanes = XAS.from_dict(site2_xanes_dict)
def setUp(self):
self.xanes = XAS.from_dict(spect_data_dict)
def test_to_from_dict(self):
s = XAS.from_dict(self.k_xanes.as_dict())
self.assertArrayAlmostEqual(s.y, self.k_xanes.y)