def test_get_spectrum_ws(self):
from mantid.simpleapi import CreateWorkspace
cfms = CrystalFieldMultiSite(['Ce'], ['C2v'],
B20=0.035,
B40=-0.012,
B43=-0.027,
B60=-0.00012,
B63=0.0025,
B66=0.0068,
Temperatures=[4.0],
FWHM=[0.1],
ToleranceIntensity=0.001 * c_mbsr)
x = np.linspace(0.0, 2.0, 30)
y = np.zeros_like(x)
e = np.ones_like(x)
ws = CreateWorkspace(x, y, e)
x, y = cfms.getSpectrum(0, ws)
y = y / c_mbsr
self.assertAlmostEqual(y[0], 12.474955, 6)
self.assertAlmostEqual(y[1], 4.300416, 6)
self.assertAlmostEqual(y[2], 1.452309, 6)
self.assertAlmostEqual(y[3], 0.692266, 6)
self.assertAlmostEqual(y[4], 0.401079, 6)
self.assertAlmostEqual(y[15], 0.050130, 6)
self.assertAlmostEqual(y[16], 0.054428, 6)
x, y = cfms.getSpectrum(ws)
y = y / c_mbsr
self.assertAlmostEqual(y[0], 12.474955, 6)
self.assertAlmostEqual(y[1], 4.300416, 6)
ws = CreateWorkspace(x, y, e, 2)
x, y = cfms.getSpectrum(ws, 1)
y = y / c_mbsr
self.assertAlmostEqual(y[0], 0.050130, 6)
self.assertAlmostEqual(y[1], 0.054428, 6)
def test_fit_multi_ion_and_spectra(self):
from CrystalField.fitting import makeWorkspace
from CrystalField import CrystalField, CrystalFieldFit
from mantid.simpleapi import CalculateChiSquared
params = {'B20': 0.37737, 'B22': 3.9770, 'B40': -0.031787, 'B42': -0.11611, 'B44': -0.12544,
'Temperature': [44.0, 50.0], 'FWHM': [1.1, 0.9]}
cf1 = CrystalField('Ce', 'C2v', **params)
cf2 = CrystalField('Pr', 'C2v', **params)
cf = cf1 + cf2
r = [0.0, 1.45, 2.4, 3.0, 3.85]
ws1 = makeWorkspace(*cf.getSpectrum(0, r))
ws2 = makeWorkspace(*cf.getSpectrum(1, r))
params = {'ion0.B20': 0.37737, 'ion0.B22': 3.9770, 'ion0.B40': -0.031787, 'ion0.B42': -0.11611,
'ion0.B44': -0.12544, 'ion1.B20': 0.37737, 'ion1.B22': 3.9770, 'ion1.B40': -0.031787,
'ion1.B42': -0.11611, 'ion1.B44': -0.12544}
cf = CrystalFieldMultiSite(Ions=['Ce', 'Pr'], Symmetries=['C2v', 'C2v'], Temperatures=[44.0, 50.0],
FWHM=[1.0, 1.0], ToleranceIntensity=6.0, ToleranceEnergy=1.0, FixAllPeaks=True,
parameters=params)
cf.fix('ion0.BmolX', 'ion0.BmolY', 'ion0.BmolZ', 'ion0.BextX', 'ion0.BextY', 'ion0.BextZ', 'ion0.B40',
'ion0.B42', 'ion0.B44', 'ion0.B60', 'ion0.B62', 'ion0.B64', 'ion0.B66', 'ion0.IntensityScaling',
'ion1.BmolX', 'ion1.BmolY', 'ion1.BmolZ', 'ion1.BextX', 'ion1.BextY', 'ion1.BextZ', 'ion1.B40',
'ion1.B42', 'ion1.B44', 'ion1.B60', 'ion1.B62', 'ion1.B64', 'ion1.B66', 'ion1.IntensityScaling',
'sp0.IntensityScaling', 'sp1.IntensityScaling')
chi2 = CalculateChiSquared(str(cf.function), InputWorkspace=ws1, InputWorkspace_1=ws2)[1]
fit = CrystalFieldFit(Model=cf, InputWorkspace=[ws1, ws2], MaxIterations=10)
fit.fit()
self.assertTrue(cf.chi2 > 0.0)
self.assertTrue(cf.chi2 < chi2)
def test_get_spectrum_ws(self):
from mantid.simpleapi import CreateWorkspace
cfms = CrystalFieldMultiSite(['Ce'], ['C2v'], B20=0.035, B40=-0.012, B43=-0.027, B60=-0.00012, B63=0.0025,
B66=0.0068, Temperatures=[4.0], FWHM=[0.1], ToleranceIntensity=0.001*c_mbsr)
x = np.linspace(0.0, 2.0, 30)
y = np.zeros_like(x)
e = np.ones_like(x)
ws = CreateWorkspace(x, y, e)
x, y = cfms.getSpectrum(0, ws)
y = y / c_mbsr
self.assertAlmostEqual(y[0], 12.474955, 6)
self.assertAlmostEqual(y[1], 4.300416, 6)
self.assertAlmostEqual(y[2], 1.452309, 6)
self.assertAlmostEqual(y[3], 0.692266, 6)
self.assertAlmostEqual(y[4], 0.401079, 6)
self.assertAlmostEqual(y[15], 0.050130, 6)
self.assertAlmostEqual(y[16], 0.054428, 6)
x, y = cfms.getSpectrum(ws)
y = y / c_mbsr
self.assertAlmostEqual(y[0], 12.474955, 6)
self.assertAlmostEqual(y[1], 4.300416, 6)
ws = CreateWorkspace(x, y, e, 2)
x, y = cfms.getSpectrum(ws, 1)
y = y / c_mbsr
self.assertAlmostEqual(y[0], 0.050130, 6)
self.assertAlmostEqual(y[1], 0.054428, 6)
def test_fit_multi_ion_and_spectra(self):
from CrystalField.fitting import makeWorkspace
from CrystalField import CrystalField, CrystalFieldFit
from mantid.simpleapi import CalculateChiSquared
params = {'B20': 0.37737, 'B22': 3.9770, 'B40': -0.031787, 'B42': -0.11611, 'B44': -0.12544,
'Temperature': [44.0, 50.0], 'FWHM': [1.1, 0.9]}
cf1 = CrystalField('Ce', 'C2v', **params)
cf2 = CrystalField('Pr', 'C2v', **params)
cf = cf1 + cf2
r = [0.0, 1.45, 2.4, 3.0, 3.85]
ws1 = makeWorkspace(*cf.getSpectrum(0, r))
ws2 = makeWorkspace(*cf.getSpectrum(1, r))
params = {'ion0.B20': 0.37737, 'ion0.B22': 3.9770, 'ion0.B40': -0.031787, 'ion0.B42': -0.11611,
'ion0.B44': -0.12544, 'ion1.B20': 0.37737, 'ion1.B22': 3.9770, 'ion1.B40': -0.031787,
'ion1.B42': -0.11611, 'ion1.B44': -0.12544}
cf = CrystalFieldMultiSite(Ions=['Ce', 'Pr'], Symmetries=['C2v', 'C2v'], Temperatures=[44.0, 50.0],
FWHM=[1.0, 1.0], ToleranceIntensity=6.0, ToleranceEnergy=1.0, FixAllPeaks=True,
parameters=params)
cf.fix('ion0.BmolX', 'ion0.BmolY', 'ion0.BmolZ', 'ion0.BextX', 'ion0.BextY', 'ion0.BextZ', 'ion0.B40',
'ion0.B42', 'ion0.B44', 'ion0.B60', 'ion0.B62', 'ion0.B64', 'ion0.B66', 'ion0.IntensityScaling',
'ion1.BmolX', 'ion1.BmolY', 'ion1.BmolZ', 'ion1.BextX', 'ion1.BextY', 'ion1.BextZ', 'ion1.B40',
'ion1.B42', 'ion1.B44', 'ion1.B60', 'ion1.B62', 'ion1.B64', 'ion1.B66', 'ion1.IntensityScaling',
'sp0.IntensityScaling', 'sp1.IntensityScaling')
chi2 = CalculateChiSquared(str(cf.function), InputWorkspace=ws1, InputWorkspace_1=ws2)[1]
fit = CrystalFieldFit(Model=cf, InputWorkspace=[ws1, ws2], MaxIterations=10)
fit.fit()
self.assertTrue(cf.chi2 > 0.0)
self.assertTrue(cf.chi2 < chi2)
def test_constraints_single_spectrum(self):
from mantid.fitfunctions import Gaussian, LinearBackground
from mantid.simpleapi import FunctionFactory
cf = CrystalFieldMultiSite(Ions=['Ce'], Symmetries=['C2v'], Temperatures=[50], FWHM=[0.9],
B20=0.37737, B22=3.9770, B40=-0.031787, B42=-0.11611, B44=-0.12544,
Background=LinearBackground(A0=1.0), BackgroundPeak=Gaussian(Height=10, Sigma=0.3))
cf.ties(B40='B20/2')
cf.constraints('IntensityScaling > 0', 'B22 < 4')
cf.constraints('pk0.FWHM < 2.2', 'pk1.FWHM >= 0.1')
cf.ties({'pk2.FWHM': '2*pk1.FWHM', 'pk3.FWHM': '2*pk2.FWHM'})
cf.background.peak.ties(Height=10.1)
cf.background.peak.constraints('Sigma > 0')
cf.background.background.ties(A0=0.1)
cf.background.background.constraints('A1 > 0')
s = cf.makeSpectrumFunction()
self.assertTrue('0<IntensityScaling' in s)
self.assertTrue('B22<4' in s)
self.assertTrue('0<bg.f0.Sigma' in s)
self.assertTrue('0<bg.f1.A1' in s)
self.assertTrue('Height=10.1' in s)
self.assertTrue('A0=0.1' in s)
self.assertTrue('pk0.FWHM<2.2' in s)
self.assertTrue('0.1<pk1.FWHM' in s)
self.assertTrue('pk2.FWHM=2*pk1.FWHM' in s)
self.assertTrue('pk3.FWHM=2*pk2.FWHM' in s)
# Test that ties and constraints are correctly defined
fun = FunctionFactory.createInitialized(s)
self.assertTrue(fun is not None)
def test_get_spectrum_list_multi_ion_and_spectra(self):
params = {
'ion0.B20': 0.37737,
'ion0.B22': 3.9770,
'ion0.B40': -0.031787,
'ion0.B42': -0.11611,
'ion0.B44': -0.12544,
'ion1.B20': 0.37737,
'ion1.B22': 3.9770,
'ion1.B40': -0.031787,
'ion1.B42': -0.11611,
'ion1.B44': -0.12544
}
cfms = CrystalFieldMultiSite(Ions=['Ce', 'Pr'],
Symmetries=['C2v', 'C2v'],
Temperatures=[44.0, 50.0],
FWHM=[1.1, 1.2],
parameters=params)
r = [0.0, 1.45, 2.4, 3.0, 3.85]
x, y = cfms.getSpectrum(0, r)
y = y / c_mbsr
expected_y = [3.904037, 0.744519, 0.274897, 0.175713, 0.106540]
np.testing.assert_equal(x, r)
np.testing.assert_almost_equal(y, expected_y, 6)
x, y = cfms.getSpectrum(1, r)
y = y / c_mbsr
expected_y = [3.704726, 0.785600, 0.296255, 0.190176, 0.115650]
np.testing.assert_equal(x, r)
np.testing.assert_almost_equal(y, expected_y, 6)
def test_add_CrystalFieldMultiSite(self):
cfms1 = CrystalFieldMultiSite(Ions=['Pm'],
Symmetries=['D2'],
Temperatures=[44, 50],
FWHM=[1.1, 0.9],
B20=0.37737,
B40=-0.031787,
B42=-0.11611,
B44=-0.15)
cfms2 = CrystalFieldMultiSite(Ions=['Ce', 'Pr'],
Symmetries=['C2v', 'C2v'],
Temperatures=[44, 50],
FWHM=[1.1, 0.9],
parameters={
'ion0.B20': 0.34,
'ion0.B22': 3.9770,
'ion1.B40': -0.03
})
cfms3 = cfms1 + cfms2
self.assertEqual(len(cfms3.Ions), 3)
self.assertEqual(len(cfms3.Symmetries), 3)
self.assertEqual(cfms3['ion0.B20'], 0.37737)
self.assertEqual(cfms3['ion1.B20'], 0.34)
self.assertEqual(cfms3['ion1.B22'], 3.9770)
self.assertEqual(cfms3['ion2.B40'], -0.03)
s = str(cfms3.function)
self.assertTrue(
'ion1.IntensityScaling=1.0*ion0.IntensityScaling' in s
or 'ion0.IntensityScaling=1.0*ion1.IntensityScaling' in s)
self.assertTrue(
'ion0.IntensityScaling=1.0*ion2.IntensityScaling' in s
or 'ion2.IntensityScaling=1.0*ion0.IntensityScaling' in s)
def test_get_spectrum_ws_multi_spectra(self):
from mantid.simpleapi import CreateWorkspace
cfms = CrystalFieldMultiSite(['Ce'], ['C2v'], B20=0.035, B40=-0.012, B43=-0.027, B60=-0.00012, B63=0.0025, B66=0.0068,
Temperatures=[4.0, 50.0], FWHM=[0.1, 0.2])
x = np.linspace(0.0, 2.0, 30)
y = np.zeros_like(x)
e = np.ones_like(x)
ws = CreateWorkspace(x, y, e)
x, y = cfms.getSpectrum(0, ws)
y = y / c_mbsr
self.assertAlmostEqual(y[0], 12.474945990071641, 6)
self.assertAlmostEqual(y[1], 4.3004130214544389, 6)
self.assertAlmostEqual(y[2], 1.4523079303712476, 6)
self.assertAlmostEqual(y[3], 0.6922657279528992, 6)
self.assertAlmostEqual(y[4], 0.40107924259746491, 6)
self.assertAlmostEqual(y[15], 0.050129858433581413, 6)
self.assertAlmostEqual(y[16], 0.054427788297191478, 6)
x, y = cfms.getSpectrum(1, ws)
y = y / c_mbsr
self.assertAlmostEqual(y[0], 6.3046623789675627, 6)
self.assertAlmostEqual(y[1], 4.2753024205094912, 6)
self.assertAlmostEqual(y[2], 2.1778204115683644, 6)
self.assertAlmostEqual(y[3], 1.2011173460849718, 6)
self.assertAlmostEqual(y[4], 0.74036730921135963, 6)
x, y = cfms.getSpectrum(ws)
y = y / c_mbsr
self.assertAlmostEqual(y[0], 12.474945990071641, 6)
self.assertAlmostEqual(y[1], 4.3004130214544389, 6)
ws = CreateWorkspace(x, y, e, 2)
x, y = cfms.getSpectrum(ws, 1)
y = y / c_mbsr
self.assertAlmostEqual(y[0], 0.050129858433581413, 6)
self.assertAlmostEqual(y[1], 0.054427788297191478, 6)
def test_fit_multi_ion_single_spectrum(self):
from CrystalField.fitting import makeWorkspace
from CrystalField import CrystalField, CrystalFieldFit
from mantid.simpleapi import CalculateChiSquared
params = {
'B20': 0.37737,
'B22': 3.9770,
'B40': -0.031787,
'B42': -0.11611,
'B44': -0.12544,
'Temperature': 44.0,
'FWHM': 1.1
}
cf1 = CrystalField('Ce', 'C2v', **params)
cf2 = CrystalField('Pr', 'C2v', **params)
cf = cf1 + cf2
r = [0.0, 1.45, 2.4, 3.0, 3.85]
x, y = cf.getSpectrum(r)
ws = makeWorkspace(x, y)
params = {
'ion0.B20': 0.37737,
'ion0.B22': 3.9770,
'ion0.B40': -0.031787,
'ion0.B42': -0.11611,
'ion0.B44': -0.12544,
'ion1.B20': 0.37737,
'ion1.B22': 3.9770,
'ion1.B40': -0.031787,
'ion1.B42': -0.11611,
'ion1.B44': -0.12544
}
cf = CrystalFieldMultiSite(Ions=['Ce', 'Pr'],
Symmetries=['C2v', 'C2v'],
Temperatures=[44.0],
FWHM=[1.1],
ToleranceIntensity=6.0,
ToleranceEnergy=1.0,
FixAllPeaks=True,
parameters=params)
cf.fix('ion0.BmolX', 'ion0.BmolY', 'ion0.BmolZ', 'ion0.BextX',
'ion0.BextY', 'ion0.BextZ', 'ion0.B40', 'ion0.B42', 'ion0.B44',
'ion0.B60', 'ion0.B62', 'ion0.B64', 'ion0.B66',
'ion0.IntensityScaling', 'ion1.BmolX', 'ion1.BmolY',
'ion1.BmolZ', 'ion1.BextX', 'ion1.BextY', 'ion1.BextZ',
'ion1.B40', 'ion1.B42', 'ion1.B44', 'ion1.B60', 'ion1.B62',
'ion1.B64', 'ion1.B66', 'ion1.IntensityScaling')
chi2 = CalculateChiSquared(cf.makeSpectrumFunction(),
InputWorkspace=ws)[1]
fit = CrystalFieldFit(Model=cf, InputWorkspace=ws, MaxIterations=10)
fit.fit()
self.assertGreater(cf.chi2, 0.0)
self.assertLess(cf.chi2, chi2)
def test_get_spectrum_from_list(self):
cfms = CrystalFieldMultiSite(Ions=['Ce'], Symmetries=['C2v'], Temperatures=[4.0], FWHM=[0.1],
B20=0.035, B40=-0.012, B43=-0.027, B60=-0.00012, B63=0.0025, B66=0.0068,
ToleranceIntensity=0.001*c_mbsr)
r = [0.0, 1.45, 2.4, 3.0, 3.85]
x, y = cfms.getSpectrum(r)
y = y / c_mbsr
expected_y = [12.474955, 1.190169, 0.122781, 0.042940, 10.837438]
np.testing.assert_equal(x, r)
np.testing.assert_almost_equal(y, expected_y, 6)
def test_get_spectrum_from_list(self):
cfms = CrystalFieldMultiSite(Ions=['Ce'], Symmetries=['C2v'], Temperatures=[4.0], FWHM=[0.1],
B20=0.035, B40=-0.012, B43=-0.027, B60=-0.00012, B63=0.0025, B66=0.0068,
ToleranceIntensity=0.001*c_mbsr)
r = [0.0, 1.45, 2.4, 3.0, 3.85]
x, y = cfms.getSpectrum(r)
y = y / c_mbsr
expected_y = [12.474955, 1.190169, 0.122781, 0.042940, 10.837438]
np.testing.assert_equal(x, r)
np.testing.assert_almost_equal(y, expected_y, 6)
def test_get_spectrum_from_list_multi_spectra(self):
cfms = CrystalFieldMultiSite(Ions=['Ce'], Symmetries=['C2v'], Temperatures=[4.0, 50.0], FWHM=[0.1, 0.2],
B20=0.035, B40=-0.012, B43=-0.027, B60=-0.00012, B63=0.0025, B66=0.0068)
r = [0.0, 1.45, 2.4, 3.0, 3.85]
x, y = cfms.getSpectrum(0, r)
y = y / c_mbsr
expected_y = [12.474946, 1.190160, 0.122785, 0.042940, 10.837170]
np.testing.assert_equal(x, r)
np.testing.assert_almost_equal(y, expected_y, 6)
x, y = cfms.getSpectrum(1, r)
y = y / c_mbsr
expected_y = [6.304662, 0.331218, 1.224681, 0.078540, 2.638049]
np.testing.assert_equal(x, r)
np.testing.assert_almost_equal(y, expected_y, 6)
def test_get_spectrum_from_list_multi_spectra(self):
cfms = CrystalFieldMultiSite(Ions=['Ce'], Symmetries=['C2v'], Temperatures=[4.0, 50.0], FWHM=[0.1, 0.2],
B20=0.035, B40=-0.012, B43=-0.027, B60=-0.00012, B63=0.0025, B66=0.0068)
r = [0.0, 1.45, 2.4, 3.0, 3.85]
x, y = cfms.getSpectrum(0, r)
y = y / c_mbsr
expected_y = [12.474946, 1.190160, 0.122785, 0.042940, 10.837170]
np.testing.assert_equal(x, r)
np.testing.assert_almost_equal(y, expected_y, 6)
x, y = cfms.getSpectrum(1, r)
y = y / c_mbsr
expected_y = [6.304662, 0.331218, 1.224681, 0.078540, 2.638049]
np.testing.assert_equal(x, r)
np.testing.assert_almost_equal(y, expected_y, 6)
def test_add_CrystalFieldSite(self):
from CrystalField import CrystalField
cfms = CrystalFieldMultiSite(Ions=['Pr'],
Symmetries=['C2v'],
Temperatures=[44, 50],
FWHM=[1.1, 0.9],
B20=0.37737,
B22=3.9770,
B40=-0.031787,
B42=-0.11611,
B44=-0.15)
params = {
'B20': 0.37737,
'B22': 3.9770,
'B40': -0.031787,
'B42': -0.11611,
'B44': -0.12544
}
cf = CrystalField('Ce', 'C2v', **params)
cf = cf * 8
cf2 = cfms + cf
self.assertEqual(cf2['ion0.B20'], 0.37737)
self.assertEqual(cf2['ion1.B20'], 0.37737)
self.assertEqual(cf2['ion0.B44'], -0.15)
self.assertEqual(cf2['ion1.B44'], -0.12544)
self.assertEqual(len(cf2.Ions), 2)
self.assertTrue('Ce' in cf2.Ions)
self.assertTrue('Pr' in cf2.Ions)
self.assertEqual(len(cf2.Symmetries), 2)
s = str(cf2.function)
self.assertTrue(
'ion0.IntensityScaling=0.125*ion1.IntensityScaling' in s)
def test_init_multi_ions(self):
cfms = CrystalFieldMultiSite(Ions=('Pm', 'Eu'), Symmetries=('D2', 'C3v'), Temperatures=[20, 52],
FWHM=[1.0, 1.0])
self.assertEqual(cfms.Ions, ['Pm', 'Eu'])
self.assertEqual(cfms.Symmetries, ['D2', 'C3v'])
self.assertEqual(cfms.Temperatures, [20, 52])
self.assertEqual(cfms.FWHM, [1.0, 1.0])
def test_set_background(self):
cf = CrystalFieldMultiSite(Ions='Ce', Symmetries='C2v', Temperatures=[20], FWHM=[1.0], Background='name=LinearBackground,A0=1')
self.assertEquals('"name=LinearBackground,A0=1"', cf['Background'])
self.assertEquals(cf.background.param['A0'], 1)
self.assertEquals(cf.background.background.param['A0'], 1)
cf.background.param['A0'] = 0
self.assertEquals(cf.background.background.param['A0'], 0)
def test_init_parameters_multi_ions(self):
cfms = CrystalFieldMultiSite(Ions=('Pm', 'Eu'), Symmetries=('D2', 'C3v'), Temperatures=[20, 52],
FWHM=[1.0, 1.0], parameters={'ion0.B40': -0.02, 'ion0.B42': -0.11,
'ion1.B42': -0.12})
self.assertEqual(cfms.function.getParameterValue('ion0.B42'), -0.11)
self.assertEqual(cfms.function.getParameterValue('ion0.B40'), -0.02)
self.assertEqual(cfms.function.getParameterValue('ion1.B42'), -0.12)
def test_set_background_composite_as_string(self):
cf = CrystalFieldMultiSite(Ions='Ce', Symmetries='C2v', Temperatures=[20], FWHM=[1.0],
Background='name=Gaussian,Height=0,PeakCentre=1,Sigma=0;name=LinearBackground,A0=0,A1=0')
self.assertEquals('"name=Gaussian,Height=0,PeakCentre=1,Sigma=0;name=LinearBackground,A0=0,A1=0"', cf['Background'])
self.assertEquals(cf.background.param['f0.Sigma'], 0)
cf.background.param['f1.A0'] = 1
self.assertEquals(cf.background.param['f1.A0'], 1)
def test_set_background_peak_only(self):
from mantid.simpleapi import Gaussian
cf = CrystalFieldMultiSite(Ions='Ce', Symmetries='C2v', Temperatures=[20], FWHM=[1.0], BackgroundPeak=Gaussian(Sigma=1))
self.assertEquals('"name=Gaussian,Height=0,PeakCentre=0,Sigma=1"', cf['Background'])
self.assertEquals(cf.background.peak.param['Sigma'], 1)
self.assertEquals(cf.background.param['Sigma'], 1)
cf.background.peak.param['Sigma'] = 0
self.assertEquals(cf.background.param['Sigma'], 0)
def test_init_single_ion(self):
cfms = CrystalFieldMultiSite(Ions='Pm',
Symmetries='D2',
Temperatures=[20, 52],
FWHM=[1.0, 1.0])
self.assertEqual(cfms.Ions, ['Pm'])
self.assertEqual(cfms.Symmetries, ['D2'])
self.assertEqual(cfms.Temperatures, [20, 52])
self.assertEqual(cfms.FWHM, [1.0, 1.0])
def test_get_spectrum_list_multi_ion_and_spectra(self):
params = {'ion0.B20': 0.37737, 'ion0.B22': 3.9770, 'ion0.B40': -0.031787, 'ion0.B42': -0.11611,
'ion0.B44': -0.12544, 'ion1.B20': 0.37737, 'ion1.B22': 3.9770, 'ion1.B40': -0.031787,
'ion1.B42': -0.11611, 'ion1.B44': -0.12544}
cfms = CrystalFieldMultiSite(Ions=['Ce', 'Pr'], Symmetries=['C2v', 'C2v'], Temperatures=[44.0, 50.0],
FWHM=[1.1, 1.2], parameters=params)
r = [0.0, 1.45, 2.4, 3.0, 3.85]
x, y = cfms.getSpectrum(0, r)
y = y / c_mbsr
expected_y = [3.904037, 0.744519, 0.274897, 0.175713, 0.106540]
np.testing.assert_equal(x, r)
np.testing.assert_almost_equal(y, expected_y, 6)
x, y = cfms.getSpectrum(1, r)
y = y / c_mbsr
expected_y = [3.704726, 0.785600, 0.296255, 0.190176, 0.115650]
np.testing.assert_equal(x, r)
np.testing.assert_almost_equal(y, expected_y, 6)
def test_peak_values_multi_ions_and_spectra(self):
cfms = CrystalFieldMultiSite(Ions=('Pm', 'Ce'), Symmetries=('D2', 'C3v'), Temperatures=[20, 52],
FWHM=[1.0, 1.0], parameters={'ion0.B40': -0.02, 'ion1.B42': -0.12})
self.assertEqual(int(cfms.function.getParameterValue('ion0.sp0.pk0.Amplitude')), 308)
self.assertEqual(cfms.function.getParameterValue('ion0.sp1.pk0.FWHM'), 1.0)
self.assertEqual(cfms.function.getParameterValue('ion0.sp0.pk1.PeakCentre'), 0)
self.assertEqual(int(cfms.function.getParameterValue('ion1.sp1.pk0.Amplitude')), 103)
self.assertEqual(cfms.function.getParameterValue('ion1.sp1.pk0.FWHM'), 1.0)
self.assertAlmostEqual(cfms.function.getParameterValue('ion1.sp0.pk1.PeakCentre'), 8.519155, 6)
def test_peak_values_multi_ions(self):
cfms = CrystalFieldMultiSite(Ions=('Pr', 'Nd'), Symmetries=('D2', 'C3v'), Temperatures=[20],
FWHM=[1.5], parameters={'ion0.B60': -0.02, 'ion1.B62': -0.12})
self.assertEqual(int(cfms.function.getParameterValue('ion0.pk0.Amplitude')), 278)
self.assertEqual(cfms.function.getParameterValue('ion0.pk0.FWHM'), 1.5)
self.assertEqual(cfms.function.getParameterValue('ion0.pk1.PeakCentre'), 982.8)
self.assertEqual(int(cfms.function.getParameterValue('ion1.pk0.Amplitude')), 234)
self.assertEqual(cfms.function.getParameterValue('ion1.pk0.FWHM'), 1.5)
self.assertAlmostEqual(cfms.function.getParameterValue('ion1.pk1.PeakCentre'), 1749.981919, 6)
def test_set_background_as_function(self):
from mantid.simpleapi import LinearBackground
cf = CrystalFieldMultiSite(Ions='Ce', Symmetries='C2v', Temperatures=[20], FWHM=[1.0],
Background=LinearBackground(A0=1))
self.assertEquals('"name=LinearBackground,A0=1,A1=0"', cf['Background'])
self.assertEquals(cf.background.param['A0'], 1)
self.assertEquals(cf.background.background.param['A0'], 1)
cf.background.param['A0'] = 0
self.assertEquals(cf.background.background.param['A0'], 0)
def test_set_background_composite(self):
from mantid.simpleapi import Gaussian, LinearBackground
cf = CrystalFieldMultiSite(Ions='Ce', Symmetries='C2v', Temperatures=[20], FWHM=[1.0],
Background= Gaussian(PeakCentre=1) + LinearBackground())
self.assertEquals('"name=Gaussian,Height=0,PeakCentre=1,Sigma=0;name=LinearBackground,A0=0,A1=0"', cf['Background'])
cf.background.param['f1.A0'] = 1
cf.background.param['f0.PeakCentre'] = 0.5
self.assertEquals(cf.background.param['f1.A0'], 1)
self.assertEquals(cf.background.param['f0.PeakCentre'], 0.5)
def test_peak_values_multi_gaussian(self):
cfms = CrystalFieldMultiSite(Ions=('Pm', 'Dy'), Symmetries=('D2', 'C3v'), Temperatures=[20, 52],
FWHM=[1.0, 1.5], parameters={'ion0.B40': -0.02, 'ion1.B42': -0.12},
PeakShape='Gaussian')
self.assertEqual(int(cfms.function.getParameterValue('ion0.sp0.pk0.Height')), 289)
self.assertAlmostEqual(cfms.function.getParameterValue('ion0.sp1.pk0.Sigma'), 0.64, 2)
self.assertEqual(cfms.function.getParameterValue('ion0.sp0.pk1.PeakCentre'), 0)
self.assertEqual(int(cfms.function.getParameterValue('ion1.sp1.pk0.Height')), 1642)
self.assertAlmostEqual(cfms.function.getParameterValue('ion1.sp1.pk0.Sigma'), 0.64, 2)
self.assertAlmostEqual(cfms.function.getParameterValue('ion1.sp0.pk1.PeakCentre'), 40.957515, 6)
def test_set_background_with_peak(self):
from mantid.simpleapi import Gaussian
cf = CrystalFieldMultiSite(Ions='Ce', Symmetries='C2v', Temperatures=[20], FWHM=[1.0], Background='name=LinearBackground', BackgroundPeak=Gaussian(Height=1))
self.assertEquals('"name=Gaussian,Height=1,PeakCentre=0,Sigma=0;name=LinearBackground"', cf['Background'])
self.assertEquals(cf.background.peak.param['Height'], 1)
self.assertEquals(cf.background.param['f0.Height'], 1)
self.assertEquals(cf.background.background.param['A0'], 0)
cf.background.peak.param['Height'] = 0
cf.background.background.param['A0'] = 1
self.assertEquals(cf.background.peak.param['Height'], 0)
self.assertEquals(cf.background.background.param['A0'], 1)
def test_peak_values(self):
cfms = CrystalFieldMultiSite(Ions='Ce',
Symmetries='C2',
Temperatures=[25],
FWHM=[1.5],
BmolX=1.0,
B40=-0.02)
self.assertEqual(int(cfms.function.getParameterValue('pk0.Amplitude')),
48)
self.assertEqual(cfms.function.getParameterValue('pk0.FWHM'), 1.5)
self.assertEqual(cfms.function.getParameterValue('pk0.PeakCentre'), 0)
def test_init_parameters(self):
cfms = CrystalFieldMultiSite(Ions='Ce',
Symmetries='C2',
Temperatures=[15],
FWHM=[1.0],
parameters={
'BmolX': 1.0,
'B40': -0.02
})
self.assertEqual(cfms.function.getParameterValue('BmolX'), 1.0)
self.assertEqual(cfms.function.getParameterValue('B40'), -0.02)
def test_get_spectrum_ws_multi_spectra(self):
from mantid.simpleapi import CreateWorkspace
cfms = CrystalFieldMultiSite(['Ce'], ['C2v'], B20=0.035, B40=-0.012, B43=-0.027, B60=-0.00012, B63=0.0025, B66=0.0068,
Temperatures=[4.0, 50.0], FWHM=[0.1, 0.2])
x = np.linspace(0.0, 2.0, 30)
y = np.zeros_like(x)
e = np.ones_like(x)
ws = CreateWorkspace(x, y, e)
x, y = cfms.getSpectrum(0, ws)
y = y / c_mbsr
self.assertAlmostEqual(y[0], 12.474945990071641, 6)
self.assertAlmostEqual(y[1], 4.3004130214544389, 6)
self.assertAlmostEqual(y[2], 1.4523079303712476, 6)
self.assertAlmostEqual(y[3], 0.6922657279528992, 6)
self.assertAlmostEqual(y[4], 0.40107924259746491, 6)
self.assertAlmostEqual(y[15], 0.050129858433581413, 6)
self.assertAlmostEqual(y[16], 0.054427788297191478, 6)
x, y = cfms.getSpectrum(1, ws)
y = y / c_mbsr
self.assertAlmostEqual(y[0], 6.3046623789675627, 6)
self.assertAlmostEqual(y[1], 4.2753024205094912, 6)
self.assertAlmostEqual(y[2], 2.1778204115683644, 6)
self.assertAlmostEqual(y[3], 1.2011173460849718, 6)
self.assertAlmostEqual(y[4], 0.74036730921135963, 6)
x, y = cfms.getSpectrum(ws)
y = y / c_mbsr
self.assertAlmostEqual(y[0], 12.474945990071641, 6)
self.assertAlmostEqual(y[1], 4.3004130214544389, 6)
ws = CreateWorkspace(x, y, e, 2)
x, y = cfms.getSpectrum(ws, 1)
y = y / c_mbsr
self.assertAlmostEqual(y[0], 0.050129858433581413, 6)
self.assertAlmostEqual(y[1], 0.054427788297191478, 6)
def test_peak_values_gaussian(self):
cfms = CrystalFieldMultiSite(Ions='Ce',
Symmetries='C2',
Temperatures=[25],
FWHM=[1.0],
PeakShape='Gaussian',
BmolX=1.0,
B40=-0.02)
self.assertEqual(int(cfms.function.getParameterValue('pk0.Height')),
45)
self.assertAlmostEqual(cfms.function.getParameterValue('pk0.Sigma'),
0.42, 2)
self.assertEqual(cfms.function.getParameterValue('pk0.PeakCentre'), 0)
def test_add_CrystalField(self):
from CrystalField import CrystalField
cfms = CrystalFieldMultiSite(Ions=['Pr'],
Symmetries=['C2v'],
Temperatures=[44, 50],
FWHM=[1.1, 0.9],
B20=0.37737,
B22=3.9770,
B40=-0.031787,
B42=-0.11611,
B44=-0.15)
params = {
'B20': 0.37737,
'B22': 3.9770,
'B40': -0.031787,
'B42': -0.11611,
'B44': -0.12544
}
cf = CrystalField('Ce', 'C2v', **params)
cf2 = cfms + cf
self.assertEqual(cf2['ion0.B20'], 0.37737)
self.assertEqual(cf2['ion1.B20'], 0.37737)
self.assertEqual(cf2['ion0.B44'], -0.15)
self.assertEqual(cf2['ion1.B44'], -0.12544)
self.assertEqual(len(cf2.Ions), 2)
self.assertTrue('Ce' in cf2.Ions)
self.assertTrue('Pr' in cf2.Ions)
self.assertEqual(len(cf2.Symmetries), 2)
s = str(cf2.function)
ties = ','.join(re.findall(r'ties=\((.*?)\)', s))
self.assertTrue(
'ion1.IntensityScaling=1.0*ion0.IntensityScaling' in ties
or 'ion0.IntensityScaling=1.0*ion1.IntensityScaling'
in ties) # either possible in python 3
def test_constraints_multi_spectrum(self):
from mantid.simpleapi import FlatBackground, Gaussian
cf = CrystalFieldMultiSite(Ions=['Ce'], Symmetries=['C2v'], Temperatures=[44, 50], FWHM=[1.1, 0.9],
Background=FlatBackground(), BackgroundPeak=Gaussian(Height=10, Sigma=0.3),
B20=0.37737, B22=3.9770, B40=-0.031787, B42=-0.11611, B44=-0.12544)
cf.constraints('sp0.IntensityScaling > 0', '0 < sp1.IntensityScaling < 2', 'B22 < 4')
cf.ties({'sp0.bg.f0.Height': 10.1})
cf.constraints('sp0.bg.f0.Sigma > 0.1')
cf.ties({'sp1.bg.f0.Height': 20.2})
cf.constraints('sp1.bg.f0.Sigma > 0.2')
cf.ties({'sp1.pk2.FWHM': '2*sp1.pk1.FWHM', 'sp1.pk3.FWHM': '2*sp1.pk2.FWHM'})
cf.constraints('sp0.pk1.FWHM < 2.2')
cf.constraints('sp1.pk1.FWHM > 1.1', '1 < sp1.pk4.FWHM < 2.2')
s = str(cf.function)
self.assertTrue('0<sp0.IntensityScaling' in s)
self.assertTrue('sp1.IntensityScaling<2' in s)
self.assertTrue('sp0.bg.f0.Height=10.1' in s)
self.assertTrue('sp1.bg.f0.Height=20.2' in s)
self.assertTrue('0.1<sp0.bg.f0.Sigma' in s)
self.assertTrue('0.2<sp1.bg.f0.Sigma' in s)
self.assertTrue('sp0.pk1.FWHM<2.2' in s)
self.assertTrue('1.1<sp1.pk1.FWHM' in s)
self.assertTrue('1<sp1.pk4.FWHM<2.2' in s)
self.assertTrue('sp1.pk2.FWHM=2*sp1.pk1.FWHM' in s)
self.assertTrue('sp1.pk3.FWHM=2*sp1.pk2.FWHM' in s)
def test_constraints_multi_spectrum_and_ion(self):
from mantid.simpleapi import FlatBackground, Gaussian
cf = CrystalFieldMultiSite(Ions=['Ce', 'Pr'],
Symmetries=['C2v', 'C2v'],
Temperatures=[44, 50],
FWHM=[1.1, 0.9],
Background=FlatBackground(),
BackgroundPeak=Gaussian(Height=10,
Sigma=0.3),
parameters={
'ion0.B20': 0.37737,
'ion0.B22': 3.9770,
'ion1.B40': -0.031787,
'ion1.B42': -0.11611,
'ion1.B44': -0.12544
})
cf.constraints('sp0.IntensityScaling > 0',
'0 < sp1.IntensityScaling < 2', 'ion0.B22 < 4')
cf.ties({'sp0.bg.f0.Height': 10.1})
cf.constraints('sp0.bg.f0.Sigma > 0.1')
cf.ties({'sp1.bg.f0.Height': 20.2})
cf.constraints('sp1.bg.f0.Sigma > 0.2')
cf.ties({
'ion0.sp1.pk2.FWHM': '2*ion0.sp1.pk1.FWHM',
'ion1.sp1.pk3.FWHM': '2*ion1.sp1.pk2.FWHM'
})
cf.constraints('ion0.sp0.pk1.FWHM < 2.2')
cf.constraints('ion0.sp1.pk1.FWHM > 1.1',
'1 < ion0.sp1.pk4.FWHM < 2.2')
s = str(cf.function)
self.assertTrue('0<sp0.IntensityScaling' in s)
self.assertTrue('sp1.IntensityScaling<2' in s)
self.assertTrue('sp0.bg.f0.Height=10.1' in s)
self.assertTrue('sp1.bg.f0.Height=20.2' in s)
self.assertTrue('0.1<sp0.bg.f0.Sigma' in s)
self.assertTrue('0.2<sp1.bg.f0.Sigma' in s)
self.assertTrue('ion0.sp0.pk1.FWHM<2.2' in s)
self.assertTrue('1.1<ion0.sp1.pk1.FWHM' in s)
self.assertTrue('1<ion0.sp1.pk4.FWHM<2.2' in s)
self.assertTrue('ion0.sp1.pk2.FWHM=2*ion0.sp1.pk1.FWHM' in s)
self.assertTrue('ion1.sp1.pk3.FWHM=2*ion1.sp1.pk2.FWHM' in s)
def test_constraints_single_spectrum(self):
from mantid.simpleapi import Gaussian, LinearBackground, FunctionFactory
cf = CrystalFieldMultiSite(Ions=['Ce'],
Symmetries=['C2v'],
Temperatures=[50],
FWHM=[0.9],
B20=0.37737,
B22=3.9770,
B40=-0.031787,
B42=-0.11611,
B44=-0.12544,
Background=LinearBackground(A0=1.0),
BackgroundPeak=Gaussian(Height=10,
Sigma=0.3))
cf.ties(B40='B20/2')
cf.constraints('IntensityScaling > 0', 'B22 < 4')
cf.constraints('pk0.FWHM < 2.2', 'pk1.FWHM >= 0.1')
cf.ties({'pk2.FWHM': '2*pk1.FWHM', 'pk3.FWHM': '2*pk2.FWHM'})
cf.background.peak.ties(Height=10.1)
cf.background.peak.constraints('Sigma > 0')
cf.background.background.ties(A0=0.1)
cf.background.background.constraints('A1 > 0')
s = cf.makeSpectrumFunction()
self.assertTrue('0<IntensityScaling' in s)
self.assertTrue('B22<4' in s)
self.assertTrue('0<bg.f0.Sigma' in s)
self.assertTrue('0<bg.f1.A1' in s)
self.assertTrue('Height=10.1' in s)
self.assertTrue('A0=0.1' in s)
self.assertTrue('pk0.FWHM<2.2' in s)
self.assertTrue('0.1<pk1.FWHM' in s)
self.assertTrue('pk2.FWHM=2*pk1.FWHM' in s)
self.assertTrue('pk3.FWHM=2*pk2.FWHM' in s)
# Test that ties and constraints are correctly defined
fun = FunctionFactory.createInitialized(s)
self.assertTrue(fun is not None)
def test_FWHM_variation_property(self):
cfms = CrystalFieldMultiSite(('Pm', 'Eu'), ('D2', 'C3v'),
FWHMVariation=0.3)
self.assertEqual(cfms.FWHMVariation, 0.3)
def test_peakShape_property(self):
cfms = CrystalFieldMultiSite(('Pm', 'Eu'), ('D2', 'C3v'),
PeakShape='Gaussian')
self.assertEqual(cfms.PeakShape, 'Gaussian')
def test_fixAllPeaks_property(self):
cfms = CrystalFieldMultiSite(('Pm', 'Eu'), ('D2', 'C3v'),
FixAllPeaks=True)
self.assertTrue(cfms.FixAllPeaks)
def test_constraints_multi_spectrum_and_ion(self):
from mantid.fitfunctions import FlatBackground, Gaussian
cf = CrystalFieldMultiSite(Ions=['Ce','Pr'], Symmetries=['C2v', 'C2v'], Temperatures=[44, 50], FWHM=[1.1, 0.9],
Background=FlatBackground(), BackgroundPeak=Gaussian(Height=10, Sigma=0.3),
parameters={'ion0.B20': 0.37737, 'ion0.B22': 3.9770, 'ion1.B40':-0.031787,
'ion1.B42':-0.11611, 'ion1.B44':-0.12544})
cf.constraints('sp0.IntensityScaling > 0', '0 < sp1.IntensityScaling < 2', 'ion0.B22 < 4')
cf.ties({'sp0.bg.f0.Height': 10.1})
cf.constraints('sp0.bg.f0.Sigma > 0.1')
cf.ties({'sp1.bg.f0.Height': 20.2})
cf.constraints('sp1.bg.f0.Sigma > 0.2')
cf.ties({'ion0.sp1.pk2.FWHM': '2*ion0.sp1.pk1.FWHM', 'ion1.sp1.pk3.FWHM': '2*ion1.sp1.pk2.FWHM'})
cf.constraints('ion0.sp0.pk1.FWHM < 2.2')
cf.constraints('ion0.sp1.pk1.FWHM > 1.1', '1 < ion0.sp1.pk4.FWHM < 2.2')
s = str(cf.function)
self.assertTrue('0<sp0.IntensityScaling' in s)
self.assertTrue('sp1.IntensityScaling<2' in s)
self.assertTrue('sp0.bg.f0.Height=10.1' in s)
self.assertTrue('sp1.bg.f0.Height=20.2' in s)
self.assertTrue('0.1<sp0.bg.f0.Sigma' in s)
self.assertTrue('0.2<sp1.bg.f0.Sigma' in s)
self.assertTrue('ion0.sp0.pk1.FWHM<2.2' in s)
self.assertTrue('1.1<ion0.sp1.pk1.FWHM' in s)
self.assertTrue('1<ion0.sp1.pk4.FWHM<2.2' in s)
self.assertTrue('ion0.sp1.pk2.FWHM=2*ion0.sp1.pk1.FWHM' in s)
self.assertTrue('ion1.sp1.pk3.FWHM=2*ion1.sp1.pk2.FWHM' in s)