Python PdfFit.read_struct_string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 read_struct_string [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 read_struct_string [as 别名]

#.........这里部分代码省略.........

    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()
        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', dcheck2)
        self.P.calc()
        G2 = numpy.array(self.P.getpdf_fit())
        r = numpy.array(self.P.getR())
        Gnoise = G1 + G2
        Gnoise[::2] += 0.01
        Gnoise[1::2] -= 0.01
        self.P.reset()
        self.P.read_struct(datafile('Ni.stru'))
        self.P.read_struct(datafile('PbScW25TiO3.stru'))
        self.P.read_data_lists('X', 0.0, 0.05, list(r), list(Gnoise))
        self.P.setphase(1)
        self.P.constrain('spdiameter', '@11')
        self.P.setphase(2)
        self.P.constrain('spdiameter', '@12')
        self.P.setpar(11, dstart1)
        self.P.setpar(12, dstart2)
        self.P.refine()
        dfinal2 = self.P.getvar('spdiameter')
        self.P.setphase(1)
        dfinal1 = self.P.getvar('spdiameter')
        self.assertAlmostEqual(dcheck1, dfinal1, 3)
        self.assertAlmostEqual(dcheck2, dfinal2, 3)
        return


    def test_spdiameter_io(self):
        """Check reading and writing of spdiameter from structure file.
        """
        import re
        self.P.read_struct(datafile('Ni.stru'))
        self.assertEqual(0.0, self.P.getvar('spdiameter'))
        # engine should not write shape factor when not defined
        spdnone = self.P.save_struct_string(1)
        self.failUnless(not re.search('(?m)^shape +sphere,', spdnone))
        self.P.setvar('spdiameter', 7)
        spd7 = self.P.save_struct_string(1)
        # spd7 should contain shape factor data
        self.failUnless(re.search('(?m)^shape +sphere,', spd7))
        self.P.reset()
        self.P.read_struct_string(spd7)
        self.assertEqual(7.0, self.P.getvar('spdiameter'))
        # try to read without comma
        spd14 = re.sub('(?m)^shape +sphere.*$', 'shape sphere 14.00', spd7)
        self.P.read_struct_string(spd14)
        self.assertEqual(14.0, self.P.getvar('spdiameter'))
        # try to read invalid shape data
        sinvalid = re.sub('(?m)^shape .*', 'shape invalid, 1', spd7)
        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 read_struct_string [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