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#!/usr/bin/env python3
"""
Fitting experimental data: spherical nanoparticles with size distribution
in 3 layers system (experiment at GALAXI).
"""
import os
import bornagain as ba
from bornagain import nm, ba_fitmonitor
from matplotlib import pyplot as plt
wavelength = 1.34*ba.angstrom
alpha_i = 0.463*ba.deg
# detector setup as given from instrument responsible
pilatus_npx, pilatus_npy = 981, 1043
pilatus_pixel_size = 0.172 # in mm
detector_distance = 1730.0 # in mm
beam_xpos, beam_ypos = 597.1, 323.4 # in pixels
datadir = os.getenv('BA_EXAMPLE_DATA_DIR', '')
if not datadir:
raise Exception("Environment variable BA_EXAMPLE_DATA_DIR not set")
# sample model
radius = 5.75*ba.nm
sigma = 0.4
distance = 53.6*ba.nm
disorder = 10.5*ba.nm
kappa = 17.5
ptfe_thickness = 22.1*ba.nm
hmdso_thickness = 18.5*ba.nm
def get_sample(params):
radius = params["radius"]
sigma = params["sigma"]
distance = params["distance"]
# defining materials
m_vacuum = ba.RefractiveMaterial("Vacuum", 0, 0)
m_Si = ba.RefractiveMaterial("Si", 5.7816e-6, 1.0229e-7)
m_Ag = ba.RefractiveMaterial("Ag", 2.2475e-5, 1.6152e-6)
m_PTFE = ba.RefractiveMaterial("PTFE", 5.20509e-6, 1.9694e-8)
m_HMDSO = ba.RefractiveMaterial("HMDSO", 2.0888e-6, 1.3261e-8)
# collection of particles with size distribution
nparticles = 20
nfwhm = 2.0
sphere_ff = ba.Sphere(radius)
sphere = ba.Particle(m_Ag, sphere_ff)
position = R3(0, 0, -1*hmdso_thickness)
sphere.translate(position)
# ln_distr = ba.DistributionLogNormal(radius, sigma)
# par_distr = ba.ParameterDistribution(
# "/Particle/Sphere/Radius", ln_distr, nparticles, nfwhm,
# part_coll = ba.ParticleDistribution(sphere, par_distr)
# interference function
interference = ba.InterferenceRadialParacrystal(
distance, 1e6*ba.nm)
interference.setKappa(kappa)
interference.setDomainSize(2e4*nm)
pdf = ba.Profile1DGauss(disorder)
interference.setProbabilityDistribution(pdf)
# assembling particle layout
layout = ba.ParticleLayout()
layout.addParticle(sphere, 1)
layout.setInterference(interference)
layout.setTotalParticleSurfaceDensity(1)
# roughness
r_ptfe = ba.LayerRoughness(2.3*ba.nm, 0.3, 5*ba.nm)
r_hmdso = ba.LayerRoughness(1.1*ba.nm, 0.3, 5*ba.nm)
# layers
vacuum_layer = ba.Layer(m_vacuum)
hmdso_layer = ba.Layer(m_HMDSO, hmdso_thickness)
hmdso_layer.addLayout(layout)
ptfe_layer = ba.Layer(m_PTFE, ptfe_thickness)
substrate_layer = ba.Layer(m_Si)
# assembling sample
sample = ba.MultiLayer()
sample.addLayer(vacuum_layer)
sample.addLayerWithTopRoughness(hmdso_layer, r_hmdso)
sample.addLayerWithTopRoughness(ptfe_layer, r_ptfe)
sample.addLayer(substrate_layer)
return sample
def create_detector():
"""
Returns a model of the GALAXY detector
"""
u0 = beam_xpos*pilatus_pixel_size # in mm
v0 = beam_ypos*pilatus_pixel_size # in mm
detector = ba.RectangularDetector(pilatus_npx,
pilatus_npx*pilatus_pixel_size,
pilatus_npy,
pilatus_npy*pilatus_pixel_size)
detector.setPerpendicularToDirectBeam(detector_distance, u0, v0)
return detector
def create_simulation(params):
"""
Creates and returns GISAS simulation with beam and detector defined
"""
beam = ba.Beam(1.2e7, wavelength, alpha_i)
sample = get_sample(params)
detector = create_detector()
simulation = ba.ScatteringSimulation(beam, sample, detector)
simulation.setRegionOfInterest(85, 70, 120, 92.)
# beamstop:
simulation.addMask(ba.Rectangle(101.9, 82.1, 103.7, 85.2), True)
return simulation
def load_real_data(filename):
"""
Loads experimental data and returns numpy array.
"""
filepath = os.path.join(datadir, filename)
return ba.IOFactory.readDatafield(filepath).npArray()
def run_fitting():
real_data = load_real_data("galaxi_data.tif.gz")
fit_objective = ba.FitObjective()
fit_objective.addSimulationAndData(create_simulation, real_data, 1)
fit_objective.initPrint(10)
observer = ba_fitmonitor.PlotterGISAS()
fit_objective.initPlot(10, observer)
params = ba.Parameters()
params.add("radius", 5.*nm, min=4, max=6, step=0.1*nm)
params.add("sigma", 0.55, min=0.2, max=0.8, step=0.01)
params.add("distance", 27.*nm, min=20, max=70)
minimizer = ba.Minimizer()
result = minimizer.minimize(fit_objective.evaluate, params)
fit_objective.finalize(result)
if __name__ == '__main__':
run_fitting()
plt.show()
|
BornAgain
≻ 20
≻ Documentation ≻ Python scripting ≻ Fitting ≻ Extended examples ≻ Experiment at GALAXI
