예제 #1
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    def test_UnitCell(self):
        structure = CrystalStructure("5.43 5.42 5.41", "F d -3 m", "Al 1/3 0.454 1/12 1.0 0.01")
        cell = structure.getUnitCell()

        self.assertEqual(cell.a(), 5.43)
        self.assertEqual(cell.b(), 5.42)
        self.assertEqual(cell.c(), 5.41)
예제 #2
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    def test_crystal_structure_handling(self):
        sample = self._ws.sample()

        self.assertEquals(sample.hasCrystalStructure(), False)
        self.assertRaises(RuntimeError, sample.getCrystalStructure)

        cs = CrystalStructure('5.43 5.43 5.43',
                              'F d -3 m',
                              'Si 0 0 0 1.0 0.01')

        sample.setCrystalStructure(cs)

        self.assertEquals(sample.hasCrystalStructure(), True)

        cs_from_sample = sample.getCrystalStructure()

        self.assertEquals(cs.getSpaceGroup().getHMSymbol(), cs_from_sample.getSpaceGroup().getHMSymbol())
        self.assertEquals(cs.getUnitCell().a(), cs_from_sample.getUnitCell().a())
        self.assertEquals(len(cs.getScatterers()), len(cs_from_sample.getScatterers()))
        self.assertEquals(cs.getScatterers()[0], cs_from_sample.getScatterers()[0])


        sample.clearCrystalStructure()

        self.assertEquals(sample.hasCrystalStructure(), False)
        self.assertRaises(RuntimeError, sample.getCrystalStructure)
예제 #3
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    def test_scatterers(self):
        initialString = "Al 1/3 0.454 1/12 1 0.01;Si 0.1 0.2 0.3 0.99 0.1"

        structure = CrystalStructure("5.43 5.42 5.41", "F d -3 m", initialString)
        scatterers = structure.getScatterers()

        self.assertEqual(';'.join(scatterers), initialString)
예제 #4
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    def test_scatterers(self):
        initialString = "Al 1/3 0.454 1/12 1 0.01;Si 0.1 0.2 0.3 0.99 0.1"

        structure = CrystalStructure("5.43 5.42 5.41", "F d -3 m",
                                     initialString)
        scatterers = structure.getScatterers()

        self.assertEqual(';'.join(scatterers), initialString)
예제 #5
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    def test_UnitCell(self):
        structure = CrystalStructure("5.43 5.42 5.41", "F d -3 m",
                                     "Al 1/3 0.454 1/12 1.0 0.01")
        cell = structure.getUnitCell()

        self.assertEqual(cell.a(), 5.43)
        self.assertEqual(cell.b(), 5.42)
        self.assertEqual(cell.c(), 5.41)
예제 #6
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class CrystalStructureTest(unittest.TestCase):
    crystalStructure = CrystalStructure("5.431 5.431 5.431", "F d -3 m", "Si 0 0 0 1.0 0.02")

    def test_create(self):
        generator = ReflectionGenerator(self.crystalStructure)
        generator = ReflectionGenerator(self.crystalStructure, ReflectionConditionFilter.Centering)

    def test_getHKLs(self):
        generator = ReflectionGenerator(self.crystalStructure)
        hkls = generator.getHKLs(1.0, 10.0)

        self.assertEqual(len(hkls), 138)

        # default is filtering by space group reflection condition
        self.assertTrue(V3D(2, 2, 2) in hkls)
        self.assertFalse(V3D(1, 0, 0) in hkls)

    def test_getHKLsUsingFilter(self):
        generator = ReflectionGenerator(self.crystalStructure)
        hkls = generator.getHKLsUsingFilter(1.0, 10.0, ReflectionConditionFilter.StructureFactor)

        self.assertEqual(len(hkls), 130)

        # The 222 is gone now
        self.assertFalse(V3D(2, 2, 2) in hkls)

    def test_getUniqueHKLs(self):
        generator = ReflectionGenerator(self.crystalStructure)
        hkls = generator.getUniqueHKLs(1.0, 10.0)

        self.assertEqual(len(hkls), 9)

        self.assertTrue(V3D(2, 2, 2) in hkls)
        self.assertFalse(V3D(1, 0, 0) in hkls)

    def test_getUniqueHKLsUsingFilter(self):
        generator = ReflectionGenerator(self.crystalStructure)
        hkls = generator.getUniqueHKLsUsingFilter(1.0, 10.0, ReflectionConditionFilter.StructureFactor)

        self.assertEqual(len(hkls), 8)
        self.assertFalse(V3D(2, 2, 2) in hkls)

    def test_getDValues(self):
        generator = ReflectionGenerator(self.crystalStructure)
        hkls = [V3D(1, 0, 0), V3D(1, 1, 1)]

        dValues = generator.getDValues(hkls)

        self.assertEqual(len(hkls), len(dValues))
        self.assertAlmostEqual(dValues[0], 5.431, places=10)
        self.assertAlmostEqual(dValues[1], 5.431 / np.sqrt(3.), places=10)

    def test_getFsSquared(self):
        generator = ReflectionGenerator(self.crystalStructure)
        hkls = generator.getUniqueHKLs(1.0, 10.0)

        fsSquared = generator.getFsSquared(hkls)

        self.assertEqual(len(fsSquared), len(hkls))
예제 #7
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 def get_generator(lattice_parameters, space_group):
     """
     """
     crystal_structure = CrystalStructure(
         ' '.join([str(x) for x in lattice_parameters]), space_group, '')
     generator = ReflectionGenerator(crystal_structure,
                                     ReflectionConditionFilter.Centering)
     return generator
예제 #8
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def _crystal_structure(ws_name, element, cif_file):
    if cif_file:
        ws = get_workspace_handle(ws_name).raw_ws
        LoadCIF(InputWorkspace=ws, InputFile=cif_file)
        return ws.sample().getCrystalStructure()
    else:
        return CrystalStructure(crystal_structure[element][0],
                                crystal_structure[element][1],
                                crystal_structure[element][2])
예제 #9
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    def test_to_string(self):
        initialString = "Al 1/3 0.454 1/12 1 0.01;Si 0.1 0.2 0.3 0.99 0.1"
        structure = CrystalStructure("5.43 5.42 5.41", "F d -3 m", initialString)

        expected_str = "Crystal structure with:\nUnit cell: a = 5.43 b = 5.42 "\
                       "c = 5.41 alpha = 90 beta = 90 gamma = 90\n"\
                       "Centering: All-face centred\nSpace Group: F d -3 m\n"\
                       "Scatterers: Al 1/3 0.454 1/12 1 0.01, "\
                       "Si 0.1 0.2 0.3 0.99 0.1"

        expected_repr = "CrystalStructure(\"5.43 5.42 5.41 90 90 90\", "\
                        "\"F d -3 m\", \"Al 1/3 0.454 1/12 1 0.01; "\
                        "Si 0.1 0.2 0.3 0.99 0.1\")"

        self.assertEqual(expected_str, str(structure))
        self.assertEqual(expected_repr, structure.__repr__())

        newStructure = eval(structure.__repr__())
        self.assertEqual(structure.getUnitCell().a(), newStructure.getUnitCell().a())
    def _update_distributions_and_weights(self):
        crystal_structure = CrystalStructure(str(self._unit_cell), str(self._space_group), str(self._atoms))
        reflection_generator = ReflectionGenerator(crystal_structure)

        # Calculate all unique reflections within the specified resolution limits, including structure factors
        unique_hkls = reflection_generator.getUniqueHKLs(self.d_min, self.d_max)
        structure_factors = reflection_generator.getFsSquared(unique_hkls)

        # Calculate multiplicities of the reflections
        point_group = crystal_structure.getSpaceGroup().getPointGroup()
        multiplicities = [len(point_group.getEquivalents(hkl)) for hkl in unique_hkls]

        # Calculate weights as F^2 * multiplicity and normalize so that Sum(weights) = 1
        weights = np.array([x * y for x, y in zip(structure_factors, multiplicities)])
        self._parameter_lock.acquire()
        self._peak_weights = weights / sum(weights)

        d_values = reflection_generator.getDValues(unique_hkls)
        self._peak_distributions = [partial(np.random.normal, loc=d, scale=self._relative_sigma * d) for d in d_values]
        self._parameter_lock.release()
예제 #11
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    def test_to_string(self):
        initialString = "Al 1/3 0.454 1/12 1 0.01;Si 0.1 0.2 0.3 0.99 0.1"
        structure = CrystalStructure("5.43 5.42 5.41", "F d -3 m",
                                     initialString)

        expected_str = "Crystal structure with:\nUnit cell: a = 5.43 b = 5.42 "\
                       "c = 5.41 alpha = 90 beta = 90 gamma = 90\n"\
                       "Centering: All-face centred\nSpace Group: F d -3 m\n"\
                       "Scatterers: Al 1/3 0.454 1/12 1 0.01, "\
                       "Si 0.1 0.2 0.3 0.99 0.1"

        expected_repr = "CrystalStructure(\"5.43 5.42 5.41 90 90 90\", "\
                        "\"F d -3 m\", \"Al 1/3 0.454 1/12 1 0.01; "\
                        "Si 0.1 0.2 0.3 0.99 0.1\")"

        self.assertEqual(expected_str, str(structure))
        self.assertEqual(expected_repr, structure.__repr__())

        newStructure = eval(structure.__repr__())
        self.assertEqual(structure.getUnitCell().a(),
                         newStructure.getUnitCell().a())
예제 #12
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    def test_crystal_structure_handling(self):
        sample = self._ws.sample()

        self.assertEquals(sample.hasCrystalStructure(), False)
        self.assertRaises(RuntimeError, sample.getCrystalStructure)

        cs = CrystalStructure('5.43 5.43 5.43',
                              'F d -3 m',
                              'Si 0 0 0 1.0 0.01')

        sample.setCrystalStructure(cs)

        self.assertEquals(sample.hasCrystalStructure(), True)

        cs_from_sample = sample.getCrystalStructure()

        self.assertEquals(cs.getSpaceGroup().getHMSymbol(), cs_from_sample.getSpaceGroup().getHMSymbol())
        self.assertEquals(cs.getUnitCell().a(), cs_from_sample.getUnitCell().a())
        self.assertEquals(len(cs.getScatterers()), len(cs_from_sample.getScatterers()))
        self.assertEquals(cs.getScatterers()[0], cs_from_sample.getScatterers()[0])


        sample.clearCrystalStructure()

        self.assertEquals(sample.hasCrystalStructure(), False)
        self.assertRaises(RuntimeError, sample.getCrystalStructure)
예제 #13
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 def _copyCrystalStructure(self, cryst):
     from mantid.geometry import CrystalStructure
     cell = cryst.getUnitCell()
     cellstr = ' '.join([
         str(v) for v in [
             cell.a(),
             cell.b(),
             cell.c(),
             cell.alpha(),
             cell.beta(),
             cell.gamma()
         ]
     ])
     return CrystalStructure(cellstr,
                             cryst.getSpaceGroup().getHMSymbol(),
                             ';'.join(cryst.getScatterers()))
예제 #14
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    def runTest(self):
        simulationWorkspace = CreateSimulationWorkspace(Instrument='WISH',
                                                        BinParams='0,1,2',
                                                        UnitX='TOF')

        SetUB(simulationWorkspace, a=5.5, b=6.5, c=8.1, u='12,1,1', v='0,4,9')

        # Setting some random crystal structure. Correctness of structure factor calculations is ensured in the
        # test suite of StructureFactorCalculator and does not need to be tested here.
        simulationWorkspace.sample().setCrystalStructure(
            CrystalStructure('5.5 6.5 8.1', 'P m m m',
                             'Fe 0.121 0.234 0.899 1.0 0.01'))

        peaks = PredictPeaks(simulationWorkspace,
                             WavelengthMin=0.5,
                             WavelengthMax=6,
                             MinDSpacing=0.5,
                             MaxDSpacing=10,
                             CalculateStructureFactors=True)

        self.assertEquals(peaks.getNumberPeaks(), self.expected_num_peaks)

        for i in range(self.expected_num_peaks):
            peak = peaks.getPeak(i)
            self.assertLessThan(0.0, peak.getIntensity())

        peaks_no_sf = PredictPeaks(simulationWorkspace,
                                   WavelengthMin=0.5,
                                   WavelengthMax=6,
                                   MinDSpacing=0.5,
                                   MaxDSpacing=10,
                                   CalculateStructureFactors=False)

        for i in range(self.expected_num_peaks):
            peak = peaks_no_sf.getPeak(i)
            self.assertEquals(0.0, peak.getIntensity())
예제 #15
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    def test_SpaceGroup(self):
        structure = CrystalStructure("5.43 5.42 5.41", "F d -3 m", "Al 1/3 0.454 1/12 1.0 0.01")
        spaceGroup = structure.getSpaceGroup()

        self.assertEqual(spaceGroup.getHMSymbol(), "F d -3 m")
예제 #16
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 def getCrystalStructure(self):
     return CrystalStructure(self.unitCell, self.spaceGroup, self.atoms)
예제 #17
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    def test_SpaceGroup(self):
        structure = CrystalStructure("5.43 5.42 5.41", "F d -3 m",
                                     "Al 1/3 0.454 1/12 1.0 0.01")
        spaceGroup = structure.getSpaceGroup()

        self.assertEqual(spaceGroup.getHMSymbol(), "F d -3 m")
예제 #18
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 def createCrystalStructureOrRaise(self, unitCell, spaceGroup, atomStrings):
     try:
         CrystalStructure(unitCell, spaceGroup, atomStrings)
         return True
     except Exception:
         return False
예제 #19
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    def runTest(self):
        from CrystalField import CrystalField, CrystalFieldFit, CrystalFieldMultiSite, Background, Function, ResolutionModel

        cf = CrystalField('Ce', 'C2v')
        cf = CrystalField('Ce', 'C2v', B20=0.37737, B22=3.9770)
        cf['B40'] = -0.031
        b = cf['B40']

        # Calculate and return the Hamiltonian matrix as a 2D numpy array.
        h = cf.getHamiltonian()
        print(h)
        # Calculate and return the eigenvalues of the Hamiltonian as a 1D numpy array.
        e = cf.getEigenvalues()
        print(e)
        # Calculate and return the eigenvectors of the Hamiltonian as a 2D numpy array.
        w = cf.getEigenvectors()
        print(w)
        # Using the keyword argument
        cf = CrystalField('Ce', 'C2v', B20=0.37737, B22=3.9770, Temperature=44)
        # Using the property
        cf.Temperature = 44

        print(cf.getPeakList())
        #[[  0.00000000e+00   2.44006198e+01   4.24977124e+01   1.80970926e+01 -2.44006198e+01]
        # [  2.16711565e+02   8.83098530e+01   5.04430056e+00   1.71153708e-01  1.41609425e-01]]
        cf.ToleranceIntensity = 1
        print(cf.getPeakList())
        #[[   0.           24.40061976   42.49771237]
        # [ 216.71156467   88.30985303    5.04430056]]
        cf.PeakShape = 'Gaussian'
        cf.FWHM = 0.9
        sp = cf.getSpectrum()
        print(cf.function)
        CrystalField_Ce = CreateWorkspace(*sp)
        print(CrystalField_Ce)

        # If the peak shape is Gaussian
        cf.peaks.param[1]['Sigma'] = 2.0
        cf.peaks.param[2]['Sigma'] = 0.01

        # If the peak shape is Lorentzian
        cf.PeakShape = 'Lorentzian'
        cf.peaks.param[1]['FWHM'] = 2.0
        cf.peaks.param[2]['FWHM'] = 0.01

        cf = CrystalField('Ce', 'C2v', B20=0.37737, B22=3.9770, B40=-0.031787, B42=-0.11611, B44=-0.12544,
                          Temperature=44.0, FWHM=1.1)
        cf.background = Background(peak=Function('Gaussian', Height=10, Sigma=1),
                                   background=Function('LinearBackground', A0=1.0, A1=0.01))
        h = cf.background.peak.param['Height']
        a1 = cf.background.background.param['A1']
        print(h)
        print(a1)

        cf.ties(B20=1.0, B40='B20/2')
        cf.constraints('1 < B22 <= 2', 'B22 < 4')

        print(cf.function[1].getTies())
        print(cf.function[1].getConstraints())

        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')

        print(cf.function[0][0].getConstraints())
        print(cf.function[0][1].getConstraints())
        print(cf.function.getTies())
        print(cf.function.getConstraints())

        cf.peaks.ties({'f2.FWHM': '2*f1.FWHM', 'f3.FWHM': '2*f2.FWHM'})
        cf.peaks.constraints('f0.FWHM < 2.2', 'f1.FWHM >= 0.1')

        cf.PeakShape = 'Gaussian'
        cf.peaks.tieAll('Sigma=0.1', 3)
        cf.peaks.constrainAll('0 < Sigma < 0.1', 4)
        cf.peaks.tieAll('Sigma=f0.Sigma', 1, 3)
        cf.peaks.ties({'f1.Sigma': 'f0.Sigma', 'f2.Sigma': 'f0.Sigma', 'f3.Sigma': 'f0.Sigma'})

        rm = ResolutionModel(([1, 2, 3, 100], [0.1, 0.3, 0.35, 2.1]))
        cf = CrystalField('Ce', 'C2v', B20=0.37737, B22=3.9770, Temperature=44.0, ResolutionModel=rm)

        rm = ResolutionModel(self.my_func, xstart=0.0, xend=24.0, accuracy=0.01)
        cf = CrystalField('Ce', 'C2v', B20=0.37737, B22=3.9770, Temperature=44.0, ResolutionModel=rm)

        marires = Instrument('MARI')
        marires.setChopper('S')
        marires.setFrequency(250)
        marires.setEi(30)
        rm = ResolutionModel(marires.getResolution, xstart=0.0, xend=29.0, accuracy=0.01)
        cf = CrystalField('Ce', 'C2v', B20=0.37737, B22=3.9770, Temperature=44.0, ResolutionModel=rm)

        cf = CrystalField('Ce', 'C2v', B20=0.37737, B22=3.9770, Temperature=44.0, ResolutionModel=rm, FWHMVariation=0.1)

        # ---------------------------

        cf = CrystalField('Ce', 'C2v', B20=0.37737, B22=3.9770, B40=-0.031787, B42=-0.11611, B44=-0.12544,
                          Temperature=[44.0, 50.], FWHM=[1.1, 0.9])
        cf.PeakShape = 'Lorentzian'
        cf.peaks[0].param[0]['FWHM'] = 1.11
        cf.peaks[1].param[1]['FWHM'] = 1.12
        cf.background = Background(peak=Function('Gaussian', Height=10, Sigma=0.3),
                                   background=Function('FlatBackground', A0=1.0))
        cf.background[1].peak.param['Sigma'] = 0.8
        cf.background[1].background.param['A0'] = 1.1

        # The B parameters are common for all spectra - syntax doesn't change
        cf.ties(B20=1.0, B40='B20/2')
        cf.constraints('1 < B22 <= 2', 'B22 < 4')

        # Backgrounds and peaks are different for different spectra - must be indexed
        cf.background[0].peak.ties(Height=10.1)
        cf.background[0].peak.constraints('Sigma > 0.1')
        cf.background[1].peak.ties(Height=20.2)
        cf.background[1].peak.constraints('Sigma > 0.2')
        cf.peaks[1].tieAll('FWHM=2*f1.FWHM', 2, 5)
        cf.peaks[0].constrainAll('FWHM < 2.2', 1, 4)

        rm = ResolutionModel([self.my_func, marires.getResolution], 0, 100, accuracy = 0.01)
        cf.ResolutionModel = rm

        # Calculate second spectrum, use the generated x-values
        sp = cf.getSpectrum(1)
        # Calculate second spectrum, use the first spectrum of a workspace
        sp = cf.getSpectrum(1, 'CrystalField_Ce')
        # Calculate first spectrum, use the i-th spectrum of a workspace
        i=0
        sp = cf.getSpectrum(0, 'CrystalField_Ce', i)

        print(cf.function)

        cf.Temperature = [5, 50, 150]

        print()
        print(cf.function)

        ws = 'CrystalField_Ce'
        ws1 = 'CrystalField_Ce'
        ws2 = 'CrystalField_Ce'
        cf = CrystalField('Ce', 'C2v', B20=0.37737, B22=3.9770, B40=-0.031787, B42=-0.11611, B44=-0.12544, Temperature=5)

        # In case of a single spectrum (ws is a workspace)
        fit = CrystalFieldFit(Model=cf, InputWorkspace=ws)

        # Or for multiple spectra
        fit = CrystalFieldFit(Model=cf, InputWorkspace=[ws1, ws2])
        cf.Temperature = [5, 50]
        fit.fit()

        params = {'B20': 0.377, 'B22': 3.9, 'B40': -0.03, 'B42': -0.116, 'B44': -0.125,
                  'Temperature': [44.0, 50.], 'FWHM': [1.1, 0.9]}
        cf1 = CrystalField('Ce', 'C2v', **params)
        cf2 = CrystalField('Pr', 'C2v', **params)
        cfms = cf1 + cf2
        cf = 2*cf1 + cf2

        cfms = CrystalFieldMultiSite(Ions=['Ce', 'Pr'], Symmetries=['C2v', 'C2v'], Temperatures=[44.0], FWHMs=[1.1])
        cfms['ion0.B40'] = -0.031
        cfms['ion1.B20'] = 0.37737
        b = cfms['ion0.B22']

        print(b)
        print(cfms.function)

        cfms = CrystalFieldMultiSite(Ions=['Ce', 'Pr'], Symmetries=['C2v', 'C2v'], Temperatures=[44.0], FWHMs=[1.1],
                                     parameters={'ion0.B20': 0.37737, 'ion0.B22': 3.9770, 'ion1.B40':-0.031787,
                                                 'ion1.B42':-0.11611, 'ion1.B44':-0.12544})
        cfms = CrystalFieldMultiSite(Ions='Ce', Symmetries='C2v', Temperatures=[20], FWHMs=[1.0],
                                     Background='name=Gaussian,Height=0,PeakCentre=1,Sigma=0;name=LinearBackground,A0=0,A1=0')
        cfms = CrystalFieldMultiSite(Ions=['Ce'], Symmetries=['C2v'], Temperatures=[50], FWHMs=[0.9],
                                     Background=LinearBackground(A0=1.0), BackgroundPeak=Gaussian(Height=10, Sigma=0.3))
        cfms = CrystalFieldMultiSite(Ions='Ce', Symmetries='C2v', Temperatures=[20], FWHMs=[1.0],
                                     Background= Gaussian(PeakCentre=1) + LinearBackground())
        cfms = CrystalFieldMultiSite(Ions=['Ce','Pr'], Symmetries=['C2v', 'C2v'], Temperatures=[44, 50], FWHMs=[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})
        cfms.ties({'sp0.bg.f0.Height': 10.1})
        cfms.constraints('sp0.bg.f0.Sigma > 0.1')
        cfms.constraints('ion0.sp0.pk1.FWHM < 2.2')
        cfms.ties({'ion0.sp1.pk2.FWHM': '2*ion0.sp1.pk1.FWHM', 'ion1.sp1.pk3.FWHM': '2*ion1.sp1.pk2.FWHM'})

        # --------------------------

        params = {'ion0.B20': 0.37737, 'ion0.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],
                                   FWHMs=[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()

        print(chi2)

        cfms = CrystalFieldMultiSite(Ions='Ce', Symmetries='C2', Temperatures=[25], FWHMs=[1.0], PeakShape='Gaussian',
                                     BmolX=1.0, B40=-0.02)
        print(str(cfms.function).split(',')[0])

        # --------------------------

        # Create some crystal field data
        origin = CrystalField('Ce', 'C2v', B20=0.37737, B22=3.9770, B40=-0.031787, B42=-0.11611, B44=-0.12544,
                              Temperature=44.0, FWHM=1.1)
        x, y = origin.getSpectrum()
        ws = makeWorkspace(x, y)

        # Define a CrystalField object with parameters slightly shifted.
        cf = CrystalField('Ce', 'C2v', B20=0, B22=0, B40=0, B42=0, B44=0,
                          Temperature=44.0, FWHM=1.0, ResolutionModel=([0, 100], [1, 1]), FWHMVariation=0)

        # Set any ties on the field parameters.
        cf.ties(B20=0.37737)
        # Create a fit object
        fit = CrystalFieldFit(cf, InputWorkspace=ws)
        # Find initial values for the field parameters.
        # You need to define the energy splitting and names of parameters to estimate.
        # Optionally additional constraints can be set on tied parameters (eg, peak centres).
        fit.estimate_parameters(EnergySplitting=50,
                                Parameters=['B22', 'B40', 'B42', 'B44'],
                                Constraints='20<f1.PeakCentre<45,20<f2.PeakCentre<45',
                                NSamples=1000)
        print('Returned', fit.get_number_estimates(), 'sets of parameters.')
        # The first set (the smallest chi squared) is selected by default.
        # Select a different parameter set if required
        fit.select_estimated_parameters(3)
        print(cf['B22'], cf['B40'], cf['B42'], cf['B44'])
        # Run fit
        fit.fit()

        # --------------------------

        from CrystalField import PointCharge
        axial_pc_model = PointCharge([[-2, 0, 0, -4], [-2, 0, 0, 4]], 'Nd')
        axial_blm = axial_pc_model.calculate()
        print(axial_blm)

        from CrystalField import PointCharge
        from mantid.geometry import CrystalStructure
        perovskite_structure = CrystalStructure('4 4 4 90 90 90', 'P m -3 m', 'Ce 0 0 0 1 0; Al 0.5 0.5 0.5 1 0; O 0.5 0.5 0 1 0')
        cubic_pc_model = PointCharge(perovskite_structure, 'Ce', Charges={'Ce':3, 'Al':3, 'O':-2}, MaxDistance=7.5)

        cubic_pc_model = PointCharge(perovskite_structure, 'Ce', Charges={'Ce':3, 'Al':3, 'O':-2}, Neighbour=2)
        print(cubic_pc_model)

        cif_pc_model = PointCharge('Sm2O3.cif')
        print(cif_pc_model.getIons())

        cif_pc_model.Charges = {'O1':-2, 'O2':-2, 'Sm1':3, 'Sm2':3, 'Sm3':3}
        cif_pc_model.IonLabel = 'Sm2'
        cif_pc_model.Neighbour = 1
        cif_blm = cif_pc_model.calculate()
        print(cif_blm)
        bad_pc_model = PointCharge('Sm2O3.cif', MaxDistance=7.5, Neighbour=2)
        print(bad_pc_model.Neighbour)
        print(bad_pc_model.MaxDistance)

        cif_pc_model.Charges = {'O':-2, 'Sm':3}
        cif_blm = cif_pc_model.calculate()
        print(cif_blm)

        cf = CrystalField('Sm', 'C2', Temperature=5, FWHM=10, **cif_pc_model.calculate())
        fit = CrystalFieldFit(cf, InputWorkspace=ws)

        fit = CrystalFieldFit(cf, InputWorkspace=ws)
        fit.fit()

        # --------------------------

        cf = CrystalField('Ce', 'C2v', B20=0.37737, B22=3.9770, Temperature=44.0)
        Cv = cf.getHeatCapacity()       # Calculates Cv(T) for 1<T<300K in 1K steps  (default)

        T = np.arange(1,900,5)
        Cv = cf.getHeatCapacity(T)      # Calculates Cv(T) for specified values of T (1 to 900K in 5K steps here)

        # Temperatures from a single spectrum workspace
        ws = CreateWorkspace(T, T, T)
        Cv = cf.getHeatCapacity(ws)     # Use the x-values of a workspace as the temperatures
        ws_cp = CreateWorkspace(*Cv)

        # Temperatures from a multi-spectrum workspace
        ws = CreateWorkspace(T, T, T, NSpec=2)
        Cv = cf.getHeatCapacity(ws, 1)  # Uses the second spectrum's x-values for T (e.g. 450<T<900)

        chi_v = cf.getSusceptibility(T, Hdir=[1, 1, 1])
        chi_v_powder = cf.getSusceptibility(T, Hdir='powder')
        chi_v_cgs = cf.getSusceptibility(T, Hdir=[1, 1, 0], Unit='SI')
        chi_v_bohr = cf.getSusceptibility(T, Unit='bohr')
        print(type([chi_v, chi_v_powder, chi_v_cgs, chi_v_bohr]))
        moment_t = cf.getMagneticMoment(Temperature=T, Hdir=[1, 1, 1], Hmag=0.1) # Calcs M(T) with at 0.1T field||[111]
        H = np.linspace(0, 30, 121)
        moment_h = cf.getMagneticMoment(Hmag=H, Hdir='powder', Temperature=10)   # Calcs M(H) at 10K for powder sample
        moment_SI = cf.getMagneticMoment(H, [1, 1, 1], Unit='SI')         # M(H) in Am^2/mol at 1K for H||[111]
        moment_cgs = cf.getMagneticMoment(100, Temperature=T, Unit='cgs') # M(T) in emu/mol in a field of 100G || [001]
        print(type([moment_t, moment_h, moment_SI, moment_cgs]))

        # --------------------------

        from CrystalField import CrystalField, CrystalFieldFit, PhysicalProperties
        # Fits a heat capacity dataset - you must have subtracted the phonon contribution by some method already
        # and the data must be in J/mol/K.
        cf = CrystalField('Ce', 'C2v', B20=0.37737, B22=3.9770, B40=-0.031787, B42=-0.11611, B44=-0.12544,
                          PhysicalProperty=PhysicalProperties('Cv'))
        fitcv = CrystalFieldFit(Model=cf, InputWorkspace=ws)
        fitcv.fit()

        params = {'B20':0.37737, 'B22':3.9770, 'B40':-0.031787, 'B42':-0.11611, 'B44':-0.12544}
        cf = CrystalField('Ce', 'C2v', **params)
        cf.PhysicalProperty = PhysicalProperties('Cv')
        fitcv = CrystalFieldFit(Model=cf, InputWorkspace=ws)
        fitcv.fit()

        # Fits a susceptibility dataset. Data is the volume susceptibility in SI units
        cf = CrystalField('Ce', 'C2v', **params)
        cf.PhysicalProperty = PhysicalProperties('susc', Hdir='powder', Unit='SI')
        fit_chi = CrystalFieldFit(Model=cf, InputWorkspace=ws)
        fit_chi.fit()

        # Fits a magnetisation dataset. Data is in emu/mol, and was measured at 5K with the field || [111].
        cf = CrystalField('Ce', 'C2v', **params)
        cf.PhysicalProperty = PhysicalProperties('M(H)', Temperature=5, Hdir=[1, 1, 1], Unit='cgs')
        fit_mag = CrystalFieldFit(Model=cf, InputWorkspace=ws)
        fit_mag.fit()

        # Fits a magnetisation vs temperature dataset. Data is in Am^2/mol, measured with a 0.1T field || [110]
        cf = CrystalField('Ce', 'C2v', **params)
        cf.PhysicalProperty = PhysicalProperties('M(T)', Hmag=0.1, Hdir=[1, 1, 0], Unit='SI')
        fit_moment = CrystalFieldFit(Model=cf, InputWorkspace=ws)
        fit_moment.fit()

        # --------------------------

        # Pregenerate the required workspaces
        for tt in [10, 44, 50]:
            cf = CrystalField('Ce', 'C2v', B20=0.37737, B22=3.9770, B40=-0.031787, B42=-0.11611, B44=-0.12544, Temperature=tt, FWHM=0.5)
            x, y = cf.getSpectrum()
            self.my_create_ws('ws_ins_'+str(tt)+'K', x, y)
        ws_ins_10K = mtd['ws_ins_10K']
        ws_ins_44K = mtd['ws_ins_44K']
        ws_ins_50K = mtd['ws_ins_50K']
        ws_cp = self.my_create_ws('ws_cp', *cf.getHeatCapacity())
        ws_chi = self.my_create_ws('ws_chi', *cf.getSusceptibility(np.linspace(1,300,100), Hdir='powder', Unit='cgs'))
        ws_mag = self.my_create_ws('ws_mag', *cf.getMagneticMoment(Hmag=np.linspace(0, 30, 100), Hdir=[1,1,1], Unit='bohr', Temperature=5))

        # --------------------------

        # Fits an INS spectrum (at 10K) and the heat capacity simultaneously
        cf = CrystalField('Ce', 'C2v', B20=0.37737, B22=3.9770, B40=-0.031787, B42=-0.11611, B44=-0.12544)
        cf.Temperature = 10
        cf.FWHM = 1.5
        cf.PhysicalProperty = PhysicalProperties('Cv')
        fit = CrystalFieldFit(Model=cf, InputWorkspace=[ws_ins_10K, ws_cp])
        fit.fit()

        # Fits two INS spectra (at 44K and 50K) and the heat capacity, susceptibility and magnetisation simultaneously.
        PPCv = PhysicalProperties('Cv')
        PPchi = PhysicalProperties('susc', 'powder', Unit='cgs')
        PPMag = PhysicalProperties('M(H)', [1, 1, 1], 5, 'bohr')
        cf = CrystalField('Ce', 'C2v', B20=0.37737, B22=3.9770, B40=-0.031787, B42=-0.11611, B44=-0.12544,
                          Temperature=[44.0, 50.], FWHM=[1.1, 0.9], PhysicalProperty=[PPCv, PPchi, PPMag] )
        fit = CrystalFieldFit(Model=cf, InputWorkspace=[ws_ins_44K, ws_ins_50K, ws_cp, ws_chi, ws_mag])
        fit.fit()