Reflectometry: Fit honeycomb lattice

In this example, we want to demonstrate how to fit a more complex sample. For this purpose, we utilize the reflectometry data of an artificial magnetic honeycomb lattice published by A. Glavic et al., in this paper

The experiment was performed with polarized neutrons, but without polarization analysis. Since the magnetization of the sample was parallel to the neutron spin, there is no spin flip and we apply the scalar theory to this problem. This is primarily done to speed up computations: when the polarized computational engine is utilized the fitting procedure takes roughly three times as long.

Experimental data

The experimental data consists of four datasets that should be fitted simultaneously. These datasets arise from the two polarization channels for up and down polarization of the incoming beam and both of these channels are measured at two temperatures (300K and 150K).

All of this is measured on the same sample, so all parameters are assumed to be the same, except the magnetization being temperature dependent. Therefore, we introduce a scaling parameter for the magnetization as the ratio of the magnetizations at 150K and 300K: $M{s150} = M{150K} / M_{300K}$.

Magnetization model

To model a magnetic material, one can assign a magnetization vector to any material, as is demonstrated in the basic polarized reflectometry tutorial. When a non-vanishing magnetization vector is specified for at least one layer in a sample, BornAgain will automatically utilize the polarized computational engine. This leads to lower performance as the computations are more invovled.

In this example, the magnetization is (anti)parallel to the neutron spin and hence we instead parametrize the magnetic layers with an effective SLD that is the sum/difference of the nuclear and their magnetic SLD:

$$\rho\pm = \rho{\text{N}} \pm \rho_{\text{M}}$$

Here the $+$ is chosen for incoming neutrons with spin up and $-$ is chosen for spin down neutrons.

Computational model

We simulate this experiment by bulding a 6 layer model: As usual the top layer is the vacuum and the bottom layer is a silicon substrate. On top of the silicon substrate, we simulate a thin oxide layer, where we fit its roughness and thickness The SLDs of these three layers are taken from the literature and kept constant.

Then we model the lattice structure with a three-layer model: two layers to account for density fluctuations in $z$-direction and another oxide layer on top. This lattice structure is assumed to be magnetic and we fit all of their SLDs, magnetic SLDs, thicknesses and roughnesses. The magnetic SLD depends on the temperature of the dataset, according to the scaling described above, where the $M_{s150}$ parameter is fitted.

All layers are modeled without absorption, i.e. no imaginary part of the SLD. Ferthermore, we apply a resolution correction as described in this tutorial with a fixed value for $\Delta Q / Q = 0.018$. The experimental data is normalized to unity, but we still fit the intensity, as is necessary due to the resolution correction.

Running a computation

In order to run a computation, we define some functions to utilize a common simulation function for the two spin channels and both temperatures:

def run_Simulation_300_p( qzs, params ):
    return run_simulation(qzs, params, sign=1)

def run_Simulation_300_m( qzs, params ):
    return run_simulation(qzs, params, sign=-1)

def run_Simulation_150_p( qzs, params ):
    return run_simulation(qzs, params, sign=1, ms150=True)

def run_Simulation_150_m( qzs, params ):
    return run_simulation(qzs, params, sign=-1, ms150=True)

Here, the given arguments specify whether we want to simulate a spin-up beam (sign = 1) and whether the scaling of the magnetization should be applied (ms150=True). For the latter, true means that a dataset at 150K is simulated while false corresponds to 300K and the scaling parameter is set to unity.

All four reflectivity curves are then computed using:

q_300_p, r_300_p = qr( run_Simulation_300_p( qzs, paramsInitial ) )
q_300_m, r_300_m = qr( run_Simulation_300_m( qzs, paramsInitial ) )

q_150_p, r_150_p = qr( run_Simulation_150_p( qzs, paramsInitial ) )
q_150_m, r_150_m = qr( run_Simulation_150_m( qzs, paramsInitial ) )

We choose some sensible initial parameters and these yield the following simulation result

Reflectivity with the initial parameters

SLD profile with the initial parameters

We have chosen the initial magnetization to be zero, hence there is only a single SLD curve for both spin directions.

Fitting

We fit this example by utilizing the differential evolution algorithm from Scipy. As a measure for the goodness of the fit, we use the relative difference:

$$\Delta = \sum_{j = 1}^4 \frac{1}{Nj} \sum{i = 1}^N \left( \frac{d{ji} - s{ji}}{d{ji} + s{ji}} \right)^2$$

Here the sum over $i$ sums up the fitting error at every data point as usual and the sum over $j$ adds the contributions from all four datasets. This is implemented in the FitObjective::__call__ function and the FitObjective object holds all four datasets, and also performs the corresponding simulations. In the function run_fit_differential_evolution this is dispatched to the differential evolution algorithm.

The given uncercainty of the experimental data is not taken into account.

Fit Result

As usual, the fit can be run with the following command:

python3 Honeycomb_fit.py fit
On a four-core workstation, the fitting procedure takes roughly 45 minutes to complete and we obtain the following result:

Reflectivity with the fit result

SLD profile with the fit result

As can be seen from the plot of the SLDs, the magnetization is indeed larger for the measurement at lower temperature, exactly as expected.

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"""
This example demonstrates how to fit a complex experimental setup using BornAgain.
It is based on real data published in  https://doi.org/10.1002/advs.201700856
by A. Glavic et al.
In this example we utilize the scalar reflectometry  engine to fit polarized 
data without spin-flip for performance reasons.
"""

import sys
import numpy
import matplotlib.pyplot as plt

from scipy.optimize import differential_evolution

import bornagain as ba
from bornagain import angstrom

from zipfile import ZipFile

# number of points on which the computed result is plotted
scan_size = 1500

# restrict the Q-range of the data used for fitting
qmin = 0.08
qmax = 1.4

####################################################################
#                  Create Sample and Simulation                    #
####################################################################


def get_sample(parameters, sign, ms150=1):

    m_Air = ba.MaterialBySLD("Air", 0, 0)
    m_PyOx  = ba.MaterialBySLD("PyOx",
                               (parameters["sld_PyOx_real"] + \
                                 sign * ms150 * parameters["msld_PyOx"] )* 1e-6,
                               parameters["sld_PyOx_imag"] * 1e-6)
    m_Py2   = ba.MaterialBySLD("Py2",
                               ( parameters["sld_Py2_real"] + \
                                 sign * ms150 * parameters["msld_Py2"] ) * 1e-6,
                               parameters["sld_Py2_imag"] * 1e-6)
    m_Py1   = ba.MaterialBySLD("Py1",
                               ( parameters["sld_Py1_real"] + \
                                 sign * ms150 * parameters["msld_Py1"] ) * 1e-6,
                               parameters["sld_Py1_imag"] * 1e-6)
    m_SiO2 = ba.MaterialBySLD("SiO2", parameters["sld_SiO2_real"]*1e-6,
                              parameters["sld_SiO2_imag"]*1e-6)
    m_Si = ba.MaterialBySLD("Substrate", parameters["sld_Si_real"]*1e-6,
                            parameters["sld_Si_imag"]*1e-6)

    l_Air = ba.Layer(m_Air)
    l_PyOx = ba.Layer(m_PyOx, parameters["t_PyOx"]*angstrom)
    l_Py2 = ba.Layer(m_Py2, parameters["t_Py2"]*angstrom)
    l_Py1 = ba.Layer(m_Py1, parameters["t_Py1"]*angstrom)
    l_SiO2 = ba.Layer(m_SiO2, parameters["t_SiO2"]*angstrom)
    l_Si = ba.Layer(m_Si)

    r_PyOx = ba.LayerRoughness()
    r_Py2 = ba.LayerRoughness()
    r_Py1 = ba.LayerRoughness()
    r_SiO2 = ba.LayerRoughness()
    r_Si = ba.LayerRoughness()

    r_PyOx.setSigma(parameters["r_PyOx"]*angstrom)
    r_Py2.setSigma(parameters["r_Py2"]*angstrom)
    r_Py1.setSigma(parameters["r_Py1"]*angstrom)
    r_SiO2.setSigma(parameters["r_SiO2"]*angstrom)
    r_Si.setSigma(parameters["r_Si"]*angstrom)

    sample = ba.MultiLayer()

    sample.addLayer(l_Air)
    sample.addLayerWithTopRoughness(l_PyOx, r_PyOx)
    sample.addLayerWithTopRoughness(l_Py2, r_Py2)
    sample.addLayerWithTopRoughness(l_Py1, r_Py1)
    sample.addLayerWithTopRoughness(l_SiO2, r_SiO2)
    sample.addLayerWithTopRoughness(l_Si, r_Si)

    sample.setRoughnessModel(ba.RoughnessModel.NEVOT_CROCE)

    return sample


def get_simulation(q_axis, fitParams, sign, ms150=False):

    n_points = 25
    n_sig = 3.0

    parameters = dict(fitParams, **fixedParams)

    q_distr = ba.RangedDistributionGaussian(n_points, n_sig)

    dq = parameters["dq"]*q_axis
    scan = ba.QSpecScan(q_axis)
    scan.setAbsoluteQResolution(q_distr, dq)

    simulation = ba.SpecularSimulation()
    simulation.setScan(scan)
    simulation.beam().setIntensity(parameters["intensity"])

    if ms150:
        sample = get_sample(parameters=parameters,
                            sign=sign,
                            ms150=parameters["ms150"])
    else:
        sample = get_sample(parameters=parameters, sign=sign, ms150=1)

    simulation.setSample(sample)
    simulation.setBackground(ba.ConstantBackground(5e-7))

    return simulation


def run_simulation(q_axis, fitParams, *, sign, ms150=False):
    simulation = get_simulation(q_axis, fitParams, sign, ms150)
    simulation.runSimulation()

    return simulation


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.result().axis(ba.Axes.QSPACE))
    r = numpy.array(result.result().array(ba.Axes.QSPACE))

    return q, r


####################################################################
#                         Plot Handling                            #
####################################################################


def plot(qs, rs, exps, shifts, labels, filename):
    """
    Plot the simulated result together with the experimental data
    """
    fig = plt.figure()
    ax = fig.add_subplot(111)

    for q, r, exp, shift, l in zip(qs, rs, exps, shifts, labels):

        ax.errorbar(exp[0],
                    exp[1]/shift,
                    yerr=exp[2]/shift,
                    fmt='.',
                    markersize=0.75,
                    linewidth=0.5)

        ax.plot(q, r/shift, label=l)

    ax.set_yscale('log')
    plt.legend()

    plt.xlabel("Q [nm${}^{-1}$]")
    plt.ylabel("R")

    plt.tight_layout()
    plt.savefig(filename)


def plot_sld_profile(fitParams, filename):

    plt.figure()
    parameters = dict(fitParams, **fixedParams)

    z_300_p, sld_300_p = ba.MaterialProfile(get_sample(parameters, 1))
    z_300_m, sld_300_m = ba.MaterialProfile(get_sample(parameters, -1))

    z_150_p, sld_150_p = ba.MaterialProfile(
        get_sample(parameters, 1, ms150=parameters["ms150"]))
    z_150_m, sld_150_m = ba.MaterialProfile(
        get_sample(parameters, -1, ms150=parameters["ms150"]))

    plt.figure()
    nsld = plt.plot(z_300_p, numpy.real(sld_300_p)*1e6, label=r"300K $+$")
    nsld = plt.plot(z_300_m, numpy.real(sld_300_m)*1e6, label=r"300K $-$")

    nsld = plt.plot(z_150_p, numpy.real(sld_150_p)*1e6, label=r"150K $+$")
    nsld = plt.plot(z_150_m, numpy.real(sld_150_m)*1e6, label=r"150K $-$")

    plt.xlabel(r"$z$ [A]")
    plt.ylabel(r"$\delta(z) \cdot 10^6$")

    plt.legend()
    plt.tight_layout()
    plt.savefig(filename)
    plt.close()


####################################################################
#                          Data Handling                           #
####################################################################


def normalizeData(data):
    """
    Removes duplicate q values from the input data,
    normalizes it such that the maximum of the reflectivity is
    unity and rescales the q-axis to inverse nm
    """
    # delete repeated data
    r0 = numpy.where(data[0] - numpy.roll(data[0], 1) == 0)
    data = numpy.delete(data, r0, 1)

    data[0] = data[0]/angstrom
    norm = numpy.max(data[1])
    data[1] = data[1]/norm
    data[2] = data[2]/norm

    # sort by q axis
    so = numpy.argsort(data[0])
    data = data[:, so]

    return data


def get_Experimental_data(filename, qmin, qmax):

    if not hasattr(get_Experimental_data, "zipfile"):
        get_Experimental_data.zipfile = ZipFile("honeycomb_data.zip")

    input_Data = numpy.genfromtxt(get_Experimental_data.zipfile.open(filename),
                                  unpack=True,
                                  usecols=(0, 2, 3))
    data = normalizeData(input_Data)

    minIndex = numpy.argmin(numpy.abs(data[0] - qmin))
    maxIndex = numpy.argmin(numpy.abs(data[0] - qmax))

    return data[:, minIndex:maxIndex + 1]


####################################################################
#                          Fit Function                            #
####################################################################


def relative_difference(sim, exp):
    result = (exp - sim)/(exp + sim)
    return numpy.sum(result*result)/len(sim)


def create_Parameter_dictionary(parameterNames, *args):
    return {name: value for name, value in zip(parameterNames, *args)}


class FitObjective:
    def __init__(self, q_axis, rdata, simulationFactory, parameterNames):
        if isinstance(q_axis, list) and isinstance(rdata, list) and \
                                    isinstance(simulationFactory, list):
            self._q = q_axis
            self._r = rdata
            self._simulationFactory = simulationFactory

        elif not isinstance(q_axis, list) and not isinstance(rdata, list) \
                              and not isinstance(simulationFactory, list):
            self._q = [q_axis]
            self._r = [rdata]
            self._simulationFactory = [simulationFactory]

        else:
            raise Exception("Inconsistent parameters")

        self._parameterNames = parameterNames

    def __call__(self, *args):
        fitParameters = create_Parameter_dictionary(self._parameterNames, *args)
        print(f"FitParamters = {fitParameters}")

        result_metric = 0

        for q, r, sim in zip(self._q, self._r, self._simulationFactory):
            sim_result = sim(q, fitParameters).result().array()
            result_metric += relative_difference(sim_result, r)

        return result_metric


def run_fit_differential_evolution(q_axis, rdata, simulationFactory,
                                   startParams):

    bounds = [(par[1], par[2]) for n, par in startParams.items()]
    parameters = [par[0] for n, par in startParams.items()]
    parameterNames = [n for n, par in startParams.items()]
    print(f"Bounds = {bounds}")

    objective = FitObjective(q_axis, rdata, simulationFactory, parameterNames)

    chi2_initial = objective(parameters)

    result = differential_evolution(objective,
                                    bounds,
                                    maxiter=200,
                                    popsize=len(bounds)*10,
                                    mutation=(0.5, 1.5),
                                    disp=True,
                                    tol=1e-2)

    resultParameters = create_Parameter_dictionary(parameterNames, result.x)
    chi2_final = objective(resultParameters.values())

    print(f"Initial chi2: {chi2_initial}")
    print(f"Final chi2: {chi2_final}")
    return resultParameters


####################################################################
#                          Main Function                           #
####################################################################

if __name__ == '__main__':

    fixedParams = {
        "sld_PyOx_imag": (0, 0, 0),
        "sld_Py2_imag": (0, 0, 0),
        "sld_Py1_imag": (0, 0, 0),
        "sld_SiO2_imag": (0, 0, 0),
        "sld_Si_imag": (0, 0, 0),
        "sld_SiO2_real": (3.47, 3, 4),
        "sld_Si_real": (2.0704, 2, 3),
        "dq": (0.018, 0.0, 0.1),
    }

    if len(sys.argv) > 1 and sys.argv[1] == "fit":

        # some sensible start parameters for fitting
        startParams = {
            "intensity": (1.04, 0, 3),
            "t_PyOx": (77, 60, 100),
            "t_Py2": (56, 40, 70),
            "t_Py1": (64, 50, 80),
            "t_SiO2": (16, 10, 30),
            "sld_PyOx_real": (1.915, 1.6, 2.2),
            "sld_Py2_real": (5.0, 3, 6),
            "sld_Py1_real": (4.62, 3, 6),
            "r_PyOx": (27, 5, 35),
            "r_Py2": (12, 5, 20),
            "r_Py1": (12, 5, 20),
            "r_SiO2": (17, 2, 25),
            "r_Si": (18, 2, 25),
            "msld_PyOx": (0.25, 0, 1),
            "msld_Py2": (0.63, 0, 1),
            "msld_Py1": (0.64, 0, 1),
            "ms150": (1, 0.9, 1.1),
        }

        fit = True

    else:
        # result from our own fitting
        startParams = {
            'intensity': 0.9482344993285265,
            't_PyOx': 74.97056190221168,
            't_Py2': 61.75823766477464,
            't_Py1': 54.058310970786316,
            't_SiO2': 23.127048588278402,
            'sld_PyOx_real': 2.199791584033569,
            'sld_Py2_real': 4.980316982224387,
            'sld_Py1_real': 4.612135848532186,
            'r_PyOx': 31.323366207013787,
            'r_Py2': 9.083768897940645,
            'r_Py1': 5.0,
            'r_SiO2': 14.43455709065263,
            'r_Si': 14.948233893986075,
            'msld_PyOx': 0.292684104601585,
            'msld_Py2': 0.5979447434271339,
            'msld_Py1': 0.56376339230351,
            'ms150': 1.083311702077648
        }

        startParams = {d: (v, ) for d, v in startParams.items()}
        fit = False

    fixedParams = {d: v[0] for d, v in fixedParams.items()}
    paramsInitial = {d: v[0] for d, v in startParams.items()}

    def run_Simulation_300_p(qzs, params):
        return run_simulation(qzs, params, sign=1)

    def run_Simulation_300_m(qzs, params):
        return run_simulation(qzs, params, sign=-1)

    def run_Simulation_150_p(qzs, params):
        return run_simulation(qzs, params, sign=1, ms150=True)

    def run_Simulation_150_m(qzs, params):
        return run_simulation(qzs, params, sign=-1, ms150=True)

    qzs = numpy.linspace(qmin, qmax, scan_size)
    q_300_p, r_300_p = qr(run_Simulation_300_p(qzs, paramsInitial))
    q_300_m, r_300_m = qr(run_Simulation_300_m(qzs, paramsInitial))

    q_150_p, r_150_p = qr(run_Simulation_150_p(qzs, paramsInitial))
    q_150_m, r_150_m = qr(run_Simulation_150_m(qzs, paramsInitial))

    data_300_p = get_Experimental_data("honeycomb_300_p.dat", qmin, qmax)
    data_300_m = get_Experimental_data("honeycomb_300_m.dat", qmin, qmax)

    data_150_p = get_Experimental_data("honeycomb_150_p.dat", qmin, qmax)
    data_150_m = get_Experimental_data("honeycomb_150_m.dat", qmin, qmax)

    plot_sld_profile(paramsInitial, f"Honeycomb_Fit_sld_profile_initial.pdf")
    plot([q_300_p, q_300_m, q_150_p, q_150_m],
         [r_300_p, r_300_m, r_150_p, r_150_m],
         [data_300_p, data_300_m, data_150_p, data_150_m], [1, 1, 10, 10],
         ["300K $+$", "300K $-$", "150K $+$", "150K $-$"],
         f"Honeycomb_Fit_reflectivity_initial.pdf")

    # fit and plot fit
    if fit:
        dataSimTuple = [[
            data_300_p[0], data_300_m[0], data_150_p[0], data_150_m[0]
        ], [data_300_p[1], data_300_m[1], data_150_p[1], data_150_m[1]],
                        [
                            run_Simulation_300_p, run_Simulation_300_m,
                            run_Simulation_150_p, run_Simulation_150_m
                        ]]

        fitResult = run_fit_differential_evolution(*dataSimTuple, startParams)

        print("Fit Result:")
        print(fitResult)

        q_300_p, r_300_p = qr(run_Simulation_300_p(qzs, fitResult))
        q_300_m, r_300_m = qr(run_Simulation_300_m(qzs, fitResult))

        q_150_p, r_150_p = qr(run_Simulation_150_p(qzs, fitResult))
        q_150_m, r_150_m = qr(run_Simulation_150_m(qzs, fitResult))

        plot([q_300_p, q_300_m, q_150_p, q_150_m],
             [r_300_p, r_300_m, r_150_p, r_150_m],
             [data_300_p, data_300_m, data_150_p, data_150_m], [1, 1, 10, 10],
             ["300K $+$", "300K $-$", "150K $+$", "150K $-$"],
             f"Honeycomb_Fit_reflectivity_fit.pdf")

        plot_sld_profile(fitResult, f"Honeycomb_Fit_sld_profile_fit.pdf")
Honeycomb_fit.py

Reference data