Python PdfFit.getvar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 getvar [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 getvar [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 getvar [as 别名]
# Load nickel structure, must be in PDFFIT or DISCUS format
pf.read_struct('Ni.stru')

# Configure Refinement -------------------------------------------------------

# Refine lattice parameters a, b, c.
# Make them all equal to parameter @1.
pf.constrain(pf.lat(1), "@1")
pf.constrain(pf.lat(2), "@1")
pf.constrain(pf.lat(3), "@1")
# set initial value of parameter @1
pf.setpar(1, pf.lat(1))

# Refine phase scale factor.  Right side can have formulas.
pf.constrain('pscale', '@20 * 2')
pf.setpar(20, pf.getvar(pf.pscale) / 2.0)

# Refine PDF damping due to instrument Q-resolution.
# Left side can be also passed as a reference to PdfFit object
pf.constrain(pf.qdamp, '@21')
pf.setpar(21, 0.03)

# Refine sharpening factor for correlated motion of close atoms.
pf.constrain(pf.delta2, 22)
pf.setpar(22, 0.0003)

# Set all temperature factors isotropic and equal to @4
for idx in range(1, 5):
    pf.constrain(pf.u11(idx), '@4')
    pf.constrain(pf.u22(idx), '@4')
    pf.constrain(pf.u33(idx), '@4')