Python PdfFit.setphase方法代码示例

# 需要导入模块: from diffpy.pdffit2 import PdfFit [as 别名]
# 或者: from diffpy.pdffit2.PdfFit import setphase [as 别名]
    def calculate(self):
        """do the real calculation
        """
        # clean up old results
        self.rcalc = []
        self.Gcalc = []

        # do the job
        if len(self.owner.strucs) == 0:
            raise ControlConfigError("No structure is given for calculation")

        # make sure parameters are initialized
        self.owner.updateParameters()
        from diffpy.pdffit2 import PdfFit
        server = PdfFit()

        # structure needs to be read before dataset allocation
        for struc in self.owner.strucs:
            server.read_struct_string(struc.writeStr('pdffit'))
            for key,var in struc.constraints.items():
                server.constrain(key.encode('ascii'), var.formula.encode('ascii'))

        # set up dataset
        server.alloc(self.stype, self.qmax, self.qdamp,
                self.rmin, self.rmax, self.rlen)
        server.setvar('qbroad', self.qbroad)
        server.setvar('dscale', self.dscale)

        # phase related variables
        # pair selection applies to current dataset,
        # therefore it has to be done after alloc
        nstrucs = len(self.owner.strucs)
        for phaseidx0, struc in enumerate(self.owner.strucs):
            phaseidx1 = phaseidx0 + 1
            server.setphase(phaseidx1)
            server.setvar('pscale', struc.getvar('pscale'))
            server.setvar('spdiameter', struc.getvar('spdiameter'))
            struc.applyPairSelection(server, phaseidx1)

        # set up parameters
        for index, par in self.owner.parameters.items():
            server.setpar(index, par.initialValue()) # info[0] = init value
            # fix if fixed.  Note: all parameters are free after server.reset().
            if par.fixed:
                server.fixpar(index)

        # all ready here
        server.calc()

        # get results
        self.rcalc = server.getR()
        self.Gcalc = server.getpdf_fit()

# 需要导入模块: from diffpy.pdffit2 import PdfFit [as 别名]
# 或者: from diffpy.pdffit2.PdfFit import setphase [as 别名]
class TestPhaseFractions(unittest.TestCase):

    places = 4

    def setUp(self):
        self.P = PdfFit()
        self.P.read_struct(datafile('Ni.stru'))
        self.P.read_struct(datafile('PbScW25TiO3.stru'))
        self.P.alloc('X', 0.0, 0.05, 0.1, 10, 200)
        self.P.alloc('N', 0.0, 0.05, 0.1, 10, 200)
        return

    def tearDown(self):
        del self.P
        return

    def test_xray_fractions(self):
        """test_xray_fractions -- check phase fractions in x-ray dataset.
        """
        self.P.setdata(1)
        ph = self.P.phase_fractions()
        bb1 = 28**2
        bb2 = ((8*82 + 24*8 + 4*21 + 2*74 + 2*22) / 40.0)**2
        self.assertAlmostEqual(1.0, sum(ph['atom']), self.places)
        self.assertAlmostEqual(1.0, sum(ph['cell']), self.places)
        self.assertAlmostEqual(1.0, sum(ph['mass']), self.places)
        self.assertAlmostEqual(bb2/bb1,
                ph['atom'][0]/ph['atom'][1], self.places)
        self.assertAlmostEqual(bb2/bb1 * 40.0/4.0,
                ph['cell'][0]/ph['cell'][1], self.places)
        mavg1 = 58.69
        mavg2 = (8*207.19 + 24*15.994 + 4*44.956 + 2*183.85 + 2*47.90)/40.0
        self.assertAlmostEqual(bb2/bb1 * mavg1/mavg2,
                ph['mass'][0]/ph['mass'][1], self.places)
        self.assertEqual(0.0, sum(ph['stdatom']))
        self.assertEqual(0.0, sum(ph['stdcell']))
        self.assertEqual(0.0, sum(ph['stdmass']))
        self.P.setphase(1)
        self.P.setvar('pscale', 2.0)
        ph2 = self.P.phase_fractions()
        self.assertAlmostEqual(1.0, sum(ph2['atom']), self.places)
        self.assertAlmostEqual(1.0, sum(ph2['cell']), self.places)
        self.assertAlmostEqual(1.0, sum(ph2['mass']), self.places)
        self.assertAlmostEqual(2.0, ph2['atom'][0]/ph2['atom'][1] /
                (ph['atom'][0]/ph['atom'][1]), self.places)
        self.assertAlmostEqual(2.0, ph2['cell'][0]/ph2['cell'][1] /
                (ph['cell'][0]/ph['cell'][1]), self.places)
        self.assertAlmostEqual(2.0, ph2['mass'][0]/ph2['mass'][1] /
                (ph['mass'][0]/ph['mass'][1]), self.places)
        return

    def test_neutron_fractions(self):
        """test_neutron_fractions -- check phase fractions in neutron dataset.
        """
        self.P.setdata(2)
        ph = self.P.phase_fractions()
        bb1 = 10.31**2
        bPb = 9.4012
        bO = 5.8054
        bSc = 12.11
        bW = 4.75518
        bTi = -3.37013
        bb2 = ((8*bPb + 24*bO + 4*bSc + 2*bW + 2*bTi) / 40.0)**2
        self.assertAlmostEqual(1.0, sum(ph['atom']), self.places)
        self.assertAlmostEqual(1.0, sum(ph['cell']), self.places)
        self.assertAlmostEqual(1.0, sum(ph['mass']), self.places)
        self.assertAlmostEqual(bb2/bb1,
                ph['atom'][0]/ph['atom'][1], self.places)
        self.assertAlmostEqual(bb2/bb1 * 40.0/4.0,
                ph['cell'][0]/ph['cell'][1], self.places)
        mavg1 = 58.69
        mavg2 = (8*207.19 + 24*15.994 + 4*44.956 + 2*183.85 + 2*47.90)/40.0
        self.assertAlmostEqual(bb2/bb1 * mavg1/mavg2,
                ph['mass'][0]/ph['mass'][1], self.places)
        self.assertEqual(0.0, sum(ph['stdatom']))
        self.assertEqual(0.0, sum(ph['stdcell']))
        self.assertEqual(0.0, sum(ph['stdmass']))
        self.P.setphase(1)
        self.P.setvar('pscale', 2.0)
        ph2 = self.P.phase_fractions()
        self.assertAlmostEqual(1.0, sum(ph2['atom']), self.places)
        self.assertAlmostEqual(1.0, sum(ph2['cell']), self.places)
        self.assertAlmostEqual(1.0, sum(ph2['mass']), self.places)
        self.assertAlmostEqual(2.0, ph2['atom'][0]/ph2['atom'][1] /
                (ph['atom'][0]/ph['atom'][1]), self.places)
        self.assertAlmostEqual(2.0, ph2['cell'][0]/ph2['cell'][1] /
                (ph['cell'][0]/ph['cell'][1]), self.places)
        self.assertAlmostEqual(2.0, ph2['mass'][0]/ph2['mass'][1] /
                (ph['mass'][0]/ph['mass'][1]), self.places)
        return

# 需要导入模块: from diffpy.pdffit2 import PdfFit [as 别名]
# 或者: from diffpy.pdffit2.PdfFit import setphase [as 别名]
class TestSphereEnvelope(unittest.TestCase):

    places = 6

    def setUp(self):
        self.P = PdfFit()
        return

    def tearDown(self):
        self.P = None
        return


    def test_calculation(self):
        """check calculation of sphere envelope factor
        """
        self.P.read_struct(datafile('Ni.stru'))
        self.P.alloc('X', 0.0, 0.05, 0.1, 10, 200)
        self.P.calc()
        d = 8.0
        r = numpy.array(self.P.getR())
        G0 = numpy.array(self.P.getpdf_fit())
        self.P.setvar('spdiameter', d)
        self.P.calc()
        G1 = numpy.array(self.P.getpdf_fit())
        dG = (G0*spherefactor(r, d) - G1)
        msd = numpy.dot(dG, dG)/len(r)
        self.assertAlmostEqual(0.0, numpy.sqrt(msd), self.places)
        return


    def test_refinement(self):
        """check refinement of sphere envelope factor
        """
        dcheck = 8.0
        dstart = 12.0
        self.P.read_struct(datafile('Ni.stru'))
        self.P.alloc('X', 0.0, 0.05, 0.1, 10, 200)
        self.P.setvar('spdiameter', dcheck)
        self.P.calc()
        r = numpy.array(self.P.getR())
        Gd8 = numpy.array(self.P.getpdf_fit())
        Gd8noise = Gd8
        Gd8noise[::2] += 0.01
        Gd8noise[1::2] -= 0.01
        self.P.reset()
        self.P.read_struct(datafile('Ni.stru'))
        self.P.read_data_lists('X', 0.0, 0.05, list(r), list(Gd8noise))
        self.P.constrain('spdiameter', '@8')
        self.P.setpar(8, dstart)
        self.P.refine()
        dfinal = self.P.getvar('spdiameter')
        self.assertAlmostEqual(dcheck, dfinal, 3)
        return


    def test_twophase_calculation(self):
        """check PDF calculation for 2 phases with different spdiameters
        """
        d1 = 6
        d2 = 9
        self.P.read_struct(datafile('Ni.stru'))
        self.P.alloc('X', 0.0, 0.05, 0.1, 10, 200)
        self.P.setvar('spdiameter', d1)
        self.P.calc()
        G1 = numpy.array(self.P.getpdf_fit())
        self.P.reset()
        self.P.read_struct(datafile('PbScW25TiO3.stru'))
        self.P.alloc('X', 0.0, 0.05, 0.1, 10, 200)
        self.P.setvar('spdiameter', d2)
        self.P.calc()
        G2 = numpy.array(self.P.getpdf_fit())
        self.P.reset()
        self.P.read_struct(datafile('Ni.stru'))
        self.P.read_struct(datafile('PbScW25TiO3.stru'))
        self.P.alloc('X', 0.0, 0.05, 0.1, 10, 200)
        self.P.setphase(1)
        self.P.setvar('spdiameter', d1)
        self.P.setphase(2)
        self.P.setvar('spdiameter', d2)
        self.P.calc()
        Gtot = numpy.array(self.P.getpdf_fit())
        dG = (G1 + G2 - Gtot)
        r = numpy.array(self.P.getR())
        msd = numpy.dot(dG, dG)/len(r)
        self.assertAlmostEqual(0.0, numpy.sqrt(msd), self.places)
        return


    def test_twophase_refinement(self):
        """check PDF refinement of 2 phases that have different spdiameter.
        """
        dcheck1 = 8.0
        dstart1 = 8.2
        dcheck2 = 6.0
        dstart2 = 5.5
        self.P.read_struct(datafile('Ni.stru'))
        self.P.alloc('X', 0.0, 0.05, 0.1, 10, 200)
        self.P.setvar('spdiameter', dcheck1)
        self.P.calc()
#.........这里部分代码省略.........

# 需要导入模块: from diffpy.pdffit2 import PdfFit [as 别名]
# 或者: from diffpy.pdffit2.PdfFit import setphase [as 别名]
class TestStepCutEnvelope(unittest.TestCase):

    places = 6

    def setUp(self):
        self.P = PdfFit()
        return

    def tearDown(self):
        self.P = None
        return


    def test_stepcut_calculation(self):
        """check calculation of sphere envelope factor
        """
        self.P.read_struct(datafile('Ni.stru'))
        self.P.alloc('X', 0.0, 0.05, 0.1, 10, 200)
        self.P.calc()
        stepcut = 8.0
        r = numpy.array(self.P.getR())
        G0 = numpy.array(self.P.getpdf_fit())
        G0[r > stepcut] = 0.0
        self.P.setvar('stepcut', stepcut)
        self.P.calc()
        G1 = numpy.array(self.P.getpdf_fit())
        dG = (G0 - G1)
        msd = numpy.dot(dG, dG)/len(r)
        self.assertAlmostEqual(0.0, numpy.sqrt(msd), self.places)
        return


    def test_twophase_stepcut_calculation(self):
        """check PDF calculation for 2 phases with different spdiameters
        """
        d1 = 6
        d2 = 9
        self.P.read_struct(datafile('Ni.stru'))
        self.P.alloc('X', 0.0, 0.05, 0.1, 10, 200)
        self.P.setvar('stepcut', d1)
        self.P.calc()
        G1 = numpy.array(self.P.getpdf_fit())
        self.P.reset()
        self.P.read_struct(datafile('PbScW25TiO3.stru'))
        self.P.alloc('X', 0.0, 0.05, 0.1, 10, 200)
        self.P.setvar('stepcut', d2)
        self.P.calc()
        G2 = numpy.array(self.P.getpdf_fit())
        self.P.reset()
        self.P.read_struct(datafile('Ni.stru'))
        self.P.read_struct(datafile('PbScW25TiO3.stru'))
        self.P.alloc('X', 0.0, 0.05, 0.1, 10, 200)
        self.P.setphase(1)
        self.P.setvar('stepcut', d1)
        self.P.setphase(2)
        self.P.setvar('stepcut', d2)
        self.P.calc()
        Gtot = numpy.array(self.P.getpdf_fit())
        dG = (G1 + G2 - Gtot)
        r = numpy.array(self.P.getR())
        msd = numpy.dot(dG, dG)/len(r)
        self.assertAlmostEqual(0.0, numpy.sqrt(msd), self.places)
        # G after step should be zero
        self.failUnless(numpy.all(0 == Gtot[r > max(d1, d2)]))
        return


    def test_stepcut_io(self):
        """Check reading and writing of stepcut from structure file.
        """
        import re
        self.P.read_struct(datafile('Ni.stru'))
        self.assertEqual(0.0, self.P.getvar('stepcut'))
        # engine should not write shape factor when not defined
        sscnone = self.P.save_struct_string(1)
        self.failUnless(not re.search('(?m)^shape +stepcut,', sscnone))
        self.P.setvar('stepcut', 7)
        ssc7 = self.P.save_struct_string(1)
        # ssc7 should contain shape factor data
        self.failUnless(re.search('(?m)^shape +stepcut,', ssc7))
        self.P.reset()
        self.P.read_struct_string(ssc7)
        self.assertEqual(7.0, self.P.getvar('stepcut'))
        # try to read without comma
        ssc14 = re.sub('(?m)^shape +stepcut.*$', 'shape stepcut 14.00', ssc7)
        self.P.read_struct_string(ssc14)
        self.assertEqual(14.0, self.P.getvar('stepcut'))
        # try to read invalid shape data
        sinvalid = re.sub('(?m)^shape .*', 'shape invalid, 1', ssc7)
        self.assertRaises(pdffit2.structureError,
                self.P.read_struct_string, sinvalid)
        return

# 需要导入模块: from diffpy.pdffit2 import PdfFit [as 别名]
# 或者: from diffpy.pdffit2.PdfFit import setphase [as 别名]

#.........这里部分代码省略.........
#       """
#       return
#
#   def test_getrw(self):
#       """check PdfFit.getrw()
#       """
#       return
#
#   def test_getR(self):
#       """check PdfFit.getR()
#       """
#       return
#
#   def test_getpdf_fit(self):
#       """check PdfFit.getpdf_fit()
#       """
#       return
#
#   def test_getpdf_obs(self):
#       """check PdfFit.getpdf_obs()
#       """
#       return
#
#   def test_getpdf_diff(self):
#       """check PdfFit.getpdf_diff()
#       """
#       return

    def test_get_atoms(self):
        """check PdfFit.get_atoms()
        """
        self.P.read_struct(datafile('Ni.stru'))
        self.P.read_struct(datafile('PbScW25TiO3.stru'))
        self.P.setphase(1)
        a1 = self.P.get_atoms()
        a2 = self.P.get_atoms(2)
        self.assertEqual(4*['NI'], a1)
        self.assertEqual(8*['PB']+24*['O']+8*['SC']+8*['W']+8*['TI'], a2)
        return

    def test_get_atom_types(self):
        """check PdfFit.get_atom_types()
        """
        self.P.read_struct(datafile('Ni.stru'))
        self.P.read_struct(datafile('PbScW25TiO3.stru'))
        self.P.setphase(1)
        atp1 = self.P.get_atom_types()
        atp2 = self.P.get_atom_types(2)
        self.assertEqual(['NI'], atp1)
        self.assertEqual(['PB', 'O', 'SC', 'W', 'TI'], atp2)
        return

    def test_num_phases(self):
        """check PdfFit.num_phases()
        """
        self.assertEqual(0, self.P.num_phases())
        self.P.read_struct(datafile('Ni.stru'))
        self.assertEqual(1, self.P.num_phases())
        self.P.read_struct(datafile('PbScW25TiO3.stru'))
        self.assertEqual(2, self.P.num_phases())
        self.P.reset()
        self.assertEqual(0, self.P.num_phases())
        return

    def test_num_datasets(self):
        """check PdfFit.num_datasets()