BornAgain

Example from Chang-Yong Kim, Chang-Yong.Kim@lightsource.ca, 21sep20

from matplotlib import pyplot as plt
import numpy as np
import bornagain as ba
from bornagain import deg, angstrom, nm, nm2, kvector_t

height = 38.66*nm
cube_sigma = 0.15
shell = 7.0 * nm
shell_sigma = 0.8
cut = 7.0 * nm
offset = 0.0
intensity = 1.0e7
background = 68.0
alpha_i = 0.1498 * deg
horizontal_slice_value = 94.0
vertical_slice_value = 81.0
x_sigma = 5.0

def get_sample(rotx):
    # Defining Materials
    material_1 = ba.HomogeneousMaterial("Air", 0.0, 0.0)
    material_2 = ba.HomogeneousMaterial("hematite", 1.557e-05, 9.418e-07)
    material_3 = ba.HomogeneousMaterial("carbon", 5.67e-06, 7.4019e-09)
    material_4 = ba.HomogeneousMaterial("Si", 6.075e-06, 1.1264e-07)

    # Defining Layers
    layer_1 = ba.Layer(material_1)
    layer_2 = ba.Layer(material_4)

    # Defining Form Factors
    formFactor_1 = ba.FormFactorBox(height, height, height)
    formFactor_2 = ba.FormFactorBox(height + 2. * shell, height + 2. * shell,
                                    height + shell + offset)

    # Defining Particles
    particle_1 = ba.Particle(material_2, formFactor_1)
    particle_2 = ba.Particle(material_3, formFactor_2)
    core_position = ba.kvector_t(0.0, 0.0, offset)

    # Set rotation around X (beam direction)
    particle_rotation = ba.RotationX(rotx * deg)
    particle_1.setRotation(particle_rotation)
    particle_2.setRotation(particle_rotation)

    # Defining Core Shell Particles
    particleCoreShell_1 = ba.ParticleCoreShell(particle_2, particle_1, core_position)
    print(particleCoreShell_1.parametersToString())

    # Defining Particle Layouts
    layout_1 = ba.ParticleLayout()
    layout_1.addParticle( particleCoreShell_1)

    # Adding layouts to layers
    layer_1.addLayout(layout_1)

    # Defining Multilayers
    multiLayer_1 = ba.MultiLayer()
    multiLayer_1.addLayer(layer_1)
    multiLayer_1.addLayer(layer_2)
    return multiLayer_1

def get_simulation(rotx):
    simulation = ba.GISASSimulation()

    detector = ba.RectangularDetector(2048, 165.0, 2048, 165.0)
    detector.setPerpendicularToDirectBeam(2367.622, 84.997, 82.338)
    simulation.setDetector(detector)

    simulation.setBeamParameters(0.1381 * nm, alpha_i, 0.0 * deg)
    simulation.setBeamIntensity(intensity)
    simulation.getOptions().setIncludeSpecular(True)
    bg = ba.ConstantBackground(background)
    simulation.setBackground(bg)

    simulation.setRegionOfInterest(45.0, 88.0, 125.0, 140.)    
    simulation.addMask(ba.Rectangle(81.86, 82.26, 88.78, 100.79), True)  # mask on reflected beam

    sample = get_sample(rotx)
    simulation.setSample(sample)

    return simulation

def run_simulation():
    hist = ba.Histogram2D(2048, 0.0, 165.0, 2048, 0.0, 165.0)
    hist_crop = hist.crop(45.0, 88.0, 125.0, 140.)

    passarg  = x_sigma
    simulation = get_simulation(passarg)
    simulation.runSimulation()

    return simulation.result()

if __name__ == '__main__':
    result = run_simulation()
    ba.plot_simulation_result(result, cmap='jet', aspect='auto')

terminate called after throwing an instance of 'std::runtime_error'
  what():  Box::createSlicedFormFactor error: not supported for the given rotation!