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# This file is part of xrayutilities.
#
# xrayutilities is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program; if not, see <http://www.gnu.org/licenses/>.
#
# Copyright (C) 2017-2021 Dominik Kriegner <dominik.kriegner@gmail.com>
import os
import unittest
from multiprocessing import freeze_support
import numpy
import xrayutilities as xu
try:
import lmfit
except ImportError:
lmfit = None
testfile = "LaB6_d500_si_psd.xye.bz2"
datadir = os.path.join(os.path.dirname(__file__), "data")
fullfilename = os.path.join(datadir, testfile)
@unittest.skipIf(
not os.path.isfile(fullfilename) or lmfit is None,
"additional test data (see http://xrayutilities.sf.io) and "
"the lmfit Python package are needed",
)
class Test_PowderModel(unittest.TestCase):
chi2max = 1.5
# define powder material
La = xu.materials.elements.La
B = xu.materials.elements.B
LaB6 = xu.materials.Crystal(
"LaB6",
xu.materials.SGLattice(
221,
4.15692,
atoms=[La, B],
pos=["1a", ("6f", 0.19750)],
b=[0.05, 0.15],
),
)
LaB6_powder = xu.simpack.Powder(
LaB6,
1,
crystallite_size_gauss=1e6,
crystallite_size_lor=0.5e-6,
strain_gauss=0,
strain_lor=0,
)
# machine settings
settings = {
"classoptions": {"oversampling": 10},
"global": {
"diffractometer_radius": 0.337,
"equatorial_divergence_deg": 0.40,
},
"tube_tails": {
"tail_left": -0.001,
"main_width": 0.00015,
"tail_right": 0.001,
"tail_intens": 0.0015,
},
"axial": {
"angI_deg": 2.0,
"angD_deg": 2.0,
"slit_length_target": 0.008,
"n_integral_points": 21,
"length_sample": 0.015,
"slit_length_source": 0.008001,
},
"si_psd": {"si_psd_window_bounds": (0, 32e-3)},
"absorption": {
"sample_thickness": 500e-6,
"absorption_coefficient": 3e4,
},
"displacement": {
"specimen_displacement": -3.8e-5,
"zero_error_deg": 0.0,
},
"emission": {"emiss_intensities": (1.0, 0.45)},
}
# define background
btt, bint = numpy.asarray(
[
(15.158, 1136.452),
(17.886, 841.925),
(22.906, 645.784),
(26.556, 551.663),
(34.554, 401.219),
(45.764, 260.595),
(58.365, 171.993),
(81.950, 112.838),
(92.370, 101.276),
(106.441, 102.486),
(126.624, 112.838),
(139.096, 132.063),
(146.240, 136.500),
(152.022, 157.204),
]
).T
def setUp(self):
with xu.io.xu_open(fullfilename) as fid:
self.tt, self.det, self.sig = numpy.loadtxt(fid, unpack=True)
self.mask = numpy.logical_and(self.tt > 18, self.tt < 148)
self.pm = xu.simpack.PowderModel(
self.LaB6_powder, I0=1.10e6, fpsettings=self.settings
)
self.pm.set_background("spline", x=self.btt, y=self.bint)
def test_Calculation(self):
x = numpy.arange(
10,
140 + numpy.random.rand() * 10,
0.0075 + numpy.random.rand() * 0.005,
)
sim = self.pm.simulate(x)
self.pm.close()
self.assertEqual(len(sim), len(x))
self.assertTrue(numpy.all(sim >= 0))
def test_multiprocessing(self):
x = numpy.arange(
10,
140 + numpy.random.rand() * 10,
0.0075 + numpy.random.rand() * 0.005,
)
st_sim = self.pm.simulate(x, mode="local")
mt_sim = self.pm.simulate(x, mode="multi")
self.pm.close()
self.assertAlmostEqual(numpy.sum(numpy.abs(st_sim - mt_sim)), 0.0)
def test_fitting(self):
# first fit run
p = self.pm.create_fitparameters()
for pn, limit in (
("primary_beam_intensity", (None, None)),
("displacement_specimen_displacement", (-1e-4, 1e-4)),
("displacement_zero_error_deg", (-0.01, 0.01)),
):
p[pn].set(vary=True, min=limit[0], max=limit[1])
fitres1 = self.pm.fit(
p,
self.tt[self.mask],
self.det[self.mask],
std=self.sig[self.mask],
maxfev=50,
)
# second fit run to optimize absorption
p = fitres1.params
for pn, limit in (
("primary_beam_intensity", (None, None)),
("displacement_specimen_displacement", (-1e-4, 1e-4)),
("absorption_absorption_coefficient", (1e4, 10e4)),
):
p[pn].set(vary=True, min=limit[0], max=limit[1])
fitres2 = self.pm.fit(
p, self.tt[self.mask], self.det[self.mask], std=self.sig[self.mask]
)
fitsim = self.pm.simulate(self.tt[self.mask])
M, Rp, Rwp, Rwpexp, chi2 = xu.simpack.Rietveld_error_metrics(
self.det[self.mask],
fitsim,
std=self.sig[self.mask],
Nvar=fitres2.nvarys,
disp=False,
)
self.pm.close()
self.assertTrue(chi2 < self.chi2max)
if __name__ == "__main__":
freeze_support() # required for MS Windows
unittest.main()
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