def test_fromStructure_CdSe(self):
"""check SFAverage.fromStructure() for CdSe
"""
cdse = loadDiffPyStructure('CdSe_cadmoselite.cif')
sfavg = SFAverage.fromStructure(cdse, self.sftx)
fcd = self.sftx.lookup('Cd')
fse = self.sftx.lookup('Se')
self.assertTrue(isinstance(sfavg.f1sum, float))
self.assertAlmostEqual(0.5 * (fcd + fse), sfavg.f1avg)
self.assertAlmostEqual(0.5 * (fcd**2 + fse**2), sfavg.f2avg)
self.assertEqual(4, sfavg.count)
self.assertEqual(cdse.composition, sfavg.composition)
qa = numpy.arange(0, 25, 0.1)
sfavg2 = SFAverage.fromStructure(cdse, self.sftx, qa)
self.assertTrue(isinstance(sfavg2.f1sum, numpy.ndarray))
self.assertNotEqual(sfavg2.f1sum[0], sfavg2.f1sum[-1])
self.assertEqual(sfavg.f1sum, sfavg2.f1sum[0])
self.assertEqual(sfavg.f2sum, sfavg2.f2sum[0])
sfavg3 = SFAverage.fromStructure(cdse, self.sftn, qa)
self.assertEqual(sfavg3.f1sum[0], sfavg3.f1sum[-1])
sfavg4 = SFAverage.fromStructure(cdse, 'N', qa)
self.assertTrue(numpy.array_equal(sfavg3.f1sum, sfavg4.f1sum))
self.assertTrue(numpy.array_equal(sfavg3.f2sum, sfavg4.f2sum))
sfavg5 = SFAverage.fromStructure(cdse, 'EN', qa)
self.assertFalse(numpy.array_equal(sfavg3.f1sum, sfavg5.f1sum))
self.assertRaises(TypeError, SFAverage.fromStructure,
'notastructure', self.sftx)
self.assertRaises(ValueError, SFAverage.fromStructure,
cdse, 'invalid')
return
def test_fromComposition(self):
"""check SFAverage.fromComposition()
"""
sfavg1 = SFAverage.fromComposition({'Na' : 1, 'Cl' : 1}, self.sftx)
fm = ['Na', 0.25, 'Cl', 0.75, 'Cl', 0.25, 'Na', 0.5, 'Na', 0.25]
smblcnts = zip(fm[0::2], fm[1::2])
sfavg2 = SFAverage.fromComposition(smblcnts, self.sftx)
self.assertEqual(sfavg1.f1sum, sfavg2.f1sum)
self.assertEqual(sfavg1.f2sum, sfavg2.f2sum)
self.assertEqual(sfavg1.count, sfavg2.count)
sfempty = SFAverage.fromComposition([], self.sftx)
self.assertEqual(0, sfempty.f1avg)
self.assertEqual(0, sfempty.f2avg)
self.assertEqual(0, sfempty.count)
return
def calc_fs_from_stru_files(*stru_files: str, qa=0) -> List[float]:
"""Calculate the compositional average scattering factor from the structure file."""
fs = []
for stru_file in stru_files:
stru = loadStructure(stru_file)
f = SFAverage.fromStructure(stru, XTB, qa).f1avg
fs.append(f)
return fs
def test_from_rutile(self):
"""check SFAverage.fromStructure for pyobjcryst Crystal of rutile.
"""
rutile = loadObjCrystCrystal('rutile.cif')
qa = numpy.arange(0, 25, 0.1)
sfavg = SFAverage.fromStructure(rutile, self.sftx, qa)
fti = self.sftx.lookup('Ti', qa)
fo = self.sftx.lookup('O', qa)
self.assertTrue(numpy.allclose((fti + 2 * fo) / 3.0, sfavg.f1avg))
fti2, fo2 = fti**2, fo**2
self.assertTrue(numpy.allclose((fti2 + 2 * fo2) / 3.0, sfavg.f2avg))
self.assertEqual(6, sfavg.count)
def calc_fs_from_comps(*comps: Formula, qa=0) -> List[float]:
"""Calculate the compositional average scattering factor from the compositions."""
def to_dict(f: Formula):
dct = {}
c = f.composition()
for tup in c:
dct[tup[0]] = tup[1]
return dct
return [
SFAverage.fromComposition(to_dict(comp), XTB, qa).f1avg
for comp in comps
]
def calc_fs_from_comps(*comps: Dict[str, int], qa=0) -> List[float]:
"""Calculate the compositional average scattering factor from the compositions."""
return [SFAverage.fromComposition(comp, XTB, qa).f1avg for comp in comps]
