Python PdfFit.getR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 getR [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 getR [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 getR [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 getR [as 别名]
class TestPdfFit(unittest.TestCase):

    places = 6

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

    def tearDown(self):
        del self.P
        return

#   def test_intro(self):
#       """check PdfFit.intro()
#       """
#       return

    def test_add_structure(self):
        """check PdfFit.add_structure()
        """
        # skip test when diffpy.Structure is not installed
        try:
            from diffpy.Structure import Structure
        except ImportError:
            return
        ni = Structure(filename=datafile('Ni.stru'))
        self.P.add_structure(ni)
        self.assertEqual(4, self.P.num_atoms())
        return

#   def test_read_struct(self):
#       """check PdfFit.read_struct()
#       """
#       return
#
#   def test_read_struct_string(self):
#       """check PdfFit.read_struct_string()
#       """
#       return
#
#   def test_read_data(self):
#       """check PdfFit.read_data()
#       """
#       return
#
#   def test_read_data_string(self):
#       """check PdfFit.read_data_string()
#       """
#       return
#
#   def test_read_data_lists(self):
#       """check PdfFit.read_data_lists()
#       """
#       return
#
#   def test_pdfrange(self):
#       """check PdfFit.pdfrange()
#       """
#       return
#
#   def test_reset(self):
#       """check PdfFit.reset()
#       """
#       return

    def test_alloc(self):
        """check PdfFit.alloc()
        """
        # alloc and read_struct can be called in any order.
        self.P.alloc('X', 25, 0.0, 0.01, 10, 1000)
        # without a structure calculated PDF is all zero
        self.P.calc()
        Gzero = self.P.getpdf_fit()
        self.assertEqual(1000*[0.0], Gzero)
        self.P.read_struct(datafile('Ni.stru'))
        self.P.calc()
        # check r-values
        r = self.P.getR()
        self.assertEqual(1000, len(r))
        for i in range(1000):
            self.assertAlmostEqual(0.01*(i + 1), r[i], self.places)
        Gfit_alloc_read = self.P.getpdf_fit()
        # now try the other order
        self.P.reset()
        self.P.read_struct(datafile('Ni.stru'))
        self.P.alloc('X', 25, 0.0, 0.01, 10, 1000)
        self.P.calc()
        Gfit_read_alloc = self.P.getpdf_fit()
        # and they should be the same
        self.assertEqual(Gfit_read_alloc, Gfit_alloc_read)
        return

#   def test_calc(self):
#       """check PdfFit.calc()
#       """
#       return
#
#   def test_refine(self):
#       """check PdfFit.refine()
#       """
#.........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 getR [as 别名]
# create new PDF calculator object
P = PdfFit()

# load structure file in PDFFIT or DISCUS format
P.read_struct("Ni.stru")

radiation_type = 'X'  # x-rays
qmax = 30.0  # Q-cutoff used in PDF calculation in 1/A
qdamp = 0.01 # instrument Q-resolution factor, responsible for PDF decay
rmin = 0.01  # minimum r-value
rmax = 30.0  # maximum r-value
npts = 3000  # number of points in the r-grid

# allocate and configure PDF calculation
P.alloc(radiation_type, qmax, qdamp, rmin, rmax, npts)
P.calc()

# obtain list of r-points and corresponding G values
r = P.getR()
G = P.getpdf_fit()

# pylab is matplotlib interface with MATLAB-like plotting commands
import pylab
pylab.plot(r, G)
pylab.xlabel('r ($\AA$)')
pylab.ylabel('G ($\AA^{-2}$)')
pylab.title('x-ray PDF of nickel simulated at Qmax = %g' % qmax)

# display plot window, this must be the last command in the script
pylab.show()

# 需要导入模块: from diffpy.pdffit2 import PdfFit [as 别名]
# 或者: from diffpy.pdffit2.PdfFit import getR [as 别名]
pf.pdfrange(1, 1.5, 19.99)
pf.refine()

# Save results ---------------------------------------------------------------

pf.save_pdf(1, "Ni_refinement.fgr")
pf.save_struct(1, "Ni_refinement.rstr")
pf.save_res("Ni_refinement.res")

# Plot results ---------------------------------------------------------------

# pylab is matplotlib interface with MATLAB-like plotting commands
import pylab

# obtain data from PdfFit calculator object
r = pf.getR()
Gobs = pf.getpdf_obs()
Gfit = pf.getpdf_fit()

# calculate difference curve, with pylab arrays it can be done
# without for loop
Gdiff = pylab.array(Gobs) - pylab.array(Gfit)
Gdiff_baseline = -10

pylab.plot(r, Gobs, 'ko')
pylab.plot(r, Gfit, 'b-')
pylab.plot(r, Gdiff + Gdiff_baseline, 'r-')

pylab.xlabel('r ($\AA$)')
pylab.ylabel('G ($\AA^{-2}$)')
pylab.title('Fit of nickel to x-ray experimental PDF')