## Cylinders in Averaged Layer

Supposing a Simulation has been defined in which some layers contain embedded particles of different materials; to regard those layers as composed by a single material, the setUseAvgMaterials method is used:

simulation.getOptions().setUseAvgMaterials(True)


The script below shows how to average materials when simulating scattering from a square lattice of cylinders inside a finite layer.

  1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68  """ Square lattice of cylinders inside finite layer with usage of average material """ import bornagain as ba from bornagain import deg, angstrom, nm def get_sample(cyl_height=5*nm): """ Returns a sample with cylinders on a substrate. """ # defining materials m_ambience = ba.HomogeneousMaterial("Air", 0.0, 0.0) m_layer = ba.HomogeneousMaterial("Layer", 3e-6, 2e-8) m_substrate = ba.HomogeneousMaterial("Substrate", 6e-6, 2e-8) m_particle = ba.HomogeneousMaterial("Particle", 3e-5, 2e-8) # cylindrical particle cylinder_ff = ba.FormFactorCylinder(5*nm, cyl_height) cylinder = ba.Particle(m_particle, cylinder_ff) position = ba.kvector_t(0.0, 0.0, -cyl_height) particle_layout = ba.ParticleLayout() particle_layout.addParticle(cylinder, 1.0, position) # interference function interference = ba.InterferenceFunction2DLattice.createSquare(15*nm) pdf = ba.FTDecayFunction2DCauchy(300*nm, 300*nm) interference.setDecayFunction(pdf) particle_layout.setInterferenceFunction(interference) air_layer = ba.Layer(m_ambience) intermediate_layer = ba.Layer(m_layer, 5*nm) intermediate_layer.addLayout(particle_layout) substrate_layer = ba.Layer(m_substrate) multi_layer = ba.MultiLayer() multi_layer.addLayer(air_layer) multi_layer.addLayer(intermediate_layer) multi_layer.addLayer(substrate_layer) return multi_layer def get_simulation(): """ Returns a GISAXS simulation with beam and detector defined """ simulation = ba.GISASSimulation() simulation.setDetectorParameters(100, -2.0*deg, 2.0*deg, 100, 0.0*deg, 2.0*deg) simulation.setBeamParameters(1.0*angstrom, 0.2*deg, 0.0*deg) simulation.getOptions().setUseAvgMaterials(True) return simulation def run_simulation(): """ Runs simulation and returns intensity map. """ simulation = get_simulation() simulation.setSample(get_sample()) simulation.runSimulation() return simulation.result() if __name__ == '__main__': result = run_simulation() ba.plot_simulation_result(result, cmap='jet', aspect='auto') 
CylindersInAverageLayer.py