issue #43: add fitting example script

examples/simpack_xrd_InAs_fitting.py

@@ -0,0 +1,71 @@
+# 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) 2019 Dominik Kriegner <dominik.kriegner@gmail.com>
+
+import xrayutilities as xu
+from matplotlib.pylab import *
+
+# global parameters
+wavelength = xu.wavelength('CuKa1')
+offset = -0.035  # angular offset of the zero position of the data
+
+# set up LayerStack for simulation: InAs(001)/(In,Mn)As(~25 nm)
+InAs = xu.materials.InAs
+InAs.lattice.a = 6.057
+lInAs = xu.simpack.Layer(InAs, inf)
+InMnAs = xu.materials.Crystal('InMnAs', xu.materials.SGLattice(
+    216, 6.050, atoms=('In', 'Mn', 'As'), pos=('4a', '4a', '4c'),
+    occ=(0.88, 0.12, 1)), cij=InAs.cij)
+lInMnAs = xu.simpack.Layer(InMnAs, 254, relaxation=0)
+pstack = xu.simpack.PseudomorphicStack001('list', lInAs, lInMnAs)
+
+# set up simulation object
+thetaMono = arcsin(wavelength/(2 * xu.materials.Ge.planeDistance(2, 2, 0)))
+Cmono = cos(2 * thetaMono)
+dyn = xu.simpack.DynamicalModel(pstack, I0=1.5e9, background=0,
+                                resolution_width=2e-3, polarization='both',
+                                Cmono=Cmono)
+fitmdyn = xu.simpack.FitModel(dyn)
+fitmdyn.set_param_hint('InMnAs_c', vary=True, min=6.02, max=6.06)
+fitmdyn.set_param_hint('InAs_a', vary=True)
+fitmdyn.set_param_hint('InMnAs_a', expr='InAs_a')
+fitmdyn.set_param_hint('resolution_width', vary=True)
+params = fitmdyn.make_params()
+
+# plot experimental data
+f = figure(figsize=(7, 5))
+d = xu.io.RASFile('inas_layer_radial_002_004.ras.bz2', path='data')
+scan = d.scans[-1]
+tt = scan.data[scan.scan_axis] - offset
+semilogy(tt, scan.data['int'], 'o-', ms=3, label='data')
+
+# perform fit and plot the result
+fitmdyn.lmodel.set_hkl((0, 0, 4))
+ai = (d.scans[-1].data[d.scan.scan_axis] - offset)/2
+fitr = fitmdyn.fit(d.scans[-1].data['int'], params, ai)
+print(fitr.fit_report())
+
+simdyn = fitmdyn.eval(fitr.params, x=tt/2)
+plot(tt, simdyn, label='sim')
+
+# label the plot
+ylabel('Intensity (counts)')
+xlabel('2Theta (deg)')
+legend()
+ylim(2e1, 1e9)
+xlim(57, 65)
+tight_layout()
+show()