diff --git a/hugo/content/installation/py/linux.md b/hugo/content/installation/py/linux.md
index e3c18e599d6a23bba78519283f9a3de2cb526a24..568bfc094db42d71436f0ade8374680c96d561c3 100644
--- a/hugo/content/installation/py/linux.md
+++ b/hugo/content/installation/py/linux.md
@@ -44,7 +44,7 @@ Then:
# install pyenv
curl https://pyenv.run | bash
-#install Python
+#install Python (e.g. {{% recommended-python %}})
pyenv install {{% recommended-python %}}
pyenv global {{% recommended-python %}}
which python # shows path in virtual environment
diff --git a/rawEx/fit/specular/PolarizedSpinAsymmetry.py b/rawEx/fit/specular/PolarizedSpinAsymmetry.py
deleted file mode 120000
index 22a16a99f0b7beba4b7ea9f1b92c54ca83437e4f..0000000000000000000000000000000000000000
--- a/rawEx/fit/specular/PolarizedSpinAsymmetry.py
+++ /dev/null
@@ -1 +0,0 @@
-../../specular/PolarizedSpinAsymmetry.py
\ No newline at end of file
diff --git a/rawEx/fit/specular/PolarizedSpinAsymmetry.py b/rawEx/fit/specular/PolarizedSpinAsymmetry.py
new file mode 100755
index 0000000000000000000000000000000000000000..56f86fc5ba316d6036c4311c56146f930463d0e1
--- /dev/null
+++ b/rawEx/fit/specular/PolarizedSpinAsymmetry.py
@@ -0,0 +1,224 @@
+#!/usr/bin/env python3
+"""
+This simulation example demonstrates how to replicate the
+fitting example "Magnetically Dead Layers in Spinel Films"
+given at the Nist website:
+https://www.nist.gov/ncnr/magnetically-dead-layers-spinel-films
+
+For simplicity, here we only reproduce the first part of that
+demonstration without the magnetically dead layer.
+"""
+
+import os
+import numpy
+import matplotlib.pyplot as plt
+import bornagain as ba
+from bornagain import angstrom, ba_plot as bp, deg, R3
+
+# q-range on which the simulation and fitting are to be performed
+qmin = 0.05997
+qmax = 1.96
+
+# number of points on which the computed result is plotted
+scan_size = 1500
+
+# The SLD of the substrate is kept constant
+sldMao = (5.377e-06, 0)
+
+# constant to convert between B and magnetic SLD
+RhoMconst = 2.910429812376859e-12
+
+####################################################################
+# Create Sample and Simulation #
+####################################################################
+
+def get_sample(P):
+ """
+ construct the sample with the given parameters
+ """
+ BMagnitude = P["rhoM_Mafo"]*1e-6/RhoMconst
+ angle = 0
+ B = R3(
+ BMagnitude*numpy.sin(angle*deg),
+ BMagnitude*numpy.cos(angle*deg), 0)
+
+ vacuum = ba.MaterialBySLD("Vacuum", 0, 0)
+ material_layer = ba.MaterialBySLD("(Mg,Al,Fe)3O4", P["rho_Mafo"]*1e-6, 0, B)
+ material_substrate = ba.MaterialBySLD("MgAl2O4", *sldMao)
+
+ ambient_layer = ba.Layer(vacuum)
+ layer = ba.Layer(material_layer, P["t_Mafo"]*angstrom)
+ substrate_layer = ba.Layer(material_substrate)
+
+ r_Mafo = ba.LayerRoughness(P["r_Mafo"]*angstrom)
+ r_substrate = ba.LayerRoughness(P["r_Mao"]*angstrom)
+
+ sample = ba.MultiLayer()
+ sample.addLayer(ambient_layer)
+ sample.addLayerWithTopRoughness(layer, r_Mafo)
+ sample.addLayerWithTopRoughness(substrate_layer, r_substrate)
+
+ return sample
+
+
+def get_simulation(sample, q_axis, parameters, polarizer_vec,
+ analyzer_vec):
+ """
+ A simulation object.
+ Polarization, analyzer and resolution are set
+ from given parameters
+ """
+ q_axis = q_axis + parameters["q_offset"]
+ distr = ba.DistributionGaussian(0., 1., 25, 4.)
+
+ scan = ba.QzScan(q_axis)
+ scan.setAbsoluteQResolution(distr, parameters["q_res"])
+ # TODO CHECK not parameters["q_res"]*q_axis ??
+
+ scan.setPolarization(polarizer_vec)
+ scan.setAnalyzer(analyzer_vec)
+
+ return ba.SpecularSimulation(scan, sample)
+
+
+def run_simulation(q_axis, fitP, *, polarizer_vec, analyzer_vec):
+ """
+ Run a simulation on the given q-axis, where the sample is
+ constructed with the given parameters.
+ Vectors for polarization and analyzer need to be provided
+ """
+ parameters = dict(fitP, **fixedP)
+
+ sample = get_sample(parameters)
+ simulation = get_simulation(sample, q_axis, parameters, polarizer_vec,
+ analyzer_vec)
+
+ return simulation.simulate()
+
+
+def qr(result):
+ """
+ Returns two arrays that hold the q-values as well as the
+ reflectivity from a given simulation result
+ """
+ q = numpy.array(result.axis(0).binCenters())
+ r = numpy.array(result.npArray())
+
+ return q, r
+
+####################################################################
+# Plot Handling #
+####################################################################
+
+def plotData(qs, rs, exps, labels, colors):
+ """
+ Plot the simulated result together with the experimental data
+ """
+ fig = plt.figure()
+ ax = fig.add_subplot(111)
+
+ for q, r, exp, l, c in zip(qs, rs, exps, labels, colors):
+ ax.errorbar(exp.xAxis().binCenters(),
+ exp.flatVector(),
+ # xerr=TODO i742,
+ yerr=exp.errorSigmas(),
+ fmt='.',
+ markersize=0.75,
+ linewidth=0.5,
+ color=c[1])
+ ax.plot(q, r, label=l, color=c[0])
+
+ ax.set_yscale('log')
+ plt.legend()
+
+ plt.xlabel(r"$q$ (nm$^{-1}$)")
+ plt.ylabel("$R$")
+
+ plt.tight_layout()
+ <%= sm ? "plt.close()" : "" %>
+
+def plotSpinAsymmetry(data_pp, data_mm, q, r_pp, r_mm):
+ """
+ Plot the simulated spin asymmetry as well its
+ experimental counterpart with errorbars
+ """
+ Yp = data_pp.npArray()
+ Ym = data_mm.npArray()
+ Ep = data_pp.npErrors()
+ Em = data_mm.npErrors()
+ # compute the errorbars of the spin asymmetry
+ delta = numpy.sqrt(4 * (Yp**2 * Em**2 + Ym**2 * Ep**2 ) / ( Yp + Ym )**4 )
+
+ fig = plt.figure()
+ ax = fig.add_subplot(111)
+
+ ax.errorbar(data_pp.xAxis().binCenters(),
+ (Yp - Ym) / (Yp + Ym),
+ # xerr=TODO i742,
+ yerr=delta,
+ fmt='.',
+ markersize=0.75,
+ linewidth=0.5)
+
+ ax.plot(q, (r_pp - r_mm)/(r_pp + r_mm))
+
+ plt.gca().set_ylim((-0.3, 0.5))
+
+ plt.xlabel(r"$q$ (nm$^{-1}$)")
+ plt.ylabel("Spin asymmetry")
+
+ plt.tight_layout()
+ <%= sm ? "plt.close()" : "" %>
+
+####################################################################
+# Data Handling #
+####################################################################
+
+def load_data(fname):
+ flags = ba.ImportSettings1D("q (1/nm)", "", "", 1, 2, 3, 4)
+ return ba.readData1D(fname, ba.csv1D, flags)
+
+####################################################################
+# Main Function #
+####################################################################
+
+if __name__ == '__main__':
+ datadir = os.getenv('BA_DATA_DIR', '')
+ fname_stem = os.path.join(datadir, "specular/MAFO_Saturated_")
+
+ expdata_pp = load_data(fname_stem + "pp.tab")
+ expdata_mm = load_data(fname_stem + "mm.tab")
+
+ fixedP = {
+ # parameters from our own fit run
+ 'q_res': 0.010542945012551425,
+ 'q_offset': 7.971243487467318e-05,
+ 'rho_Mafo': 6.370140108715461,
+ 'rhoM_Mafo': 0.27399566816062926,
+ 't_Mafo': 137.46913056084736,
+ 'r_Mao': 8.60487712674644,
+ 'r_Mafo': 3.7844265311293483
+ }
+
+ def run_Simulation_pp(qzs, P):
+ return run_simulation(qzs,
+ P,
+ polarizer_vec=R3(0, 1, 0),
+ analyzer_vec=R3(0, 1, 0))
+
+ def run_Simulation_mm(qzs, P):
+ return run_simulation(qzs,
+ P,
+ polarizer_vec=R3(0, -1, 0),
+ analyzer_vec=R3(0, -1, 0))
+
+ qzs = numpy.linspace(qmin, qmax, scan_size)
+ q_pp, r_pp = qr(run_Simulation_pp(qzs, fixedP))
+ q_mm, r_mm = qr(run_Simulation_mm(qzs, fixedP))
+
+ plotData([q_pp, q_mm], [r_pp, r_mm], [expdata_pp, expdata_mm],
+ ["$++$", "$--$"], [['orange','red'], ['green','blue']])
+
+ plotSpinAsymmetry(expdata_pp, expdata_mm, qzs, r_pp, r_mm)
+
+ bp.show_or_export()