def get_sample(): """ Returns a sample with cylinders in a homogeneous medium ("Vacuum"). The cylinders are a 95:5 mixture of two different size distributions. """ # defining materials m_vacuum = ba.HomogeneousMaterial("Vacuum", 0.0, 0.0) m_particle = ba.HomogeneousMaterial("Particle", 6e-4, 2e-8) # collection of particles #1 radius1 = 5.0 * nm height1 = radius1 sigma1 = radius1 * 0.2 cylinder_ff1 = ba.FormFactorCylinder(radius1, height1) cylinder1 = ba.Particle(m_particle, cylinder_ff1) gauss_distr1 = ba.DistributionGaussian(radius1, sigma1) nparticles = 150 sigma_factor = 3.0 # limits will assure, that generated Radius'es are >=0 limits = ba.RealLimits.nonnegative() par_distr1 = ba.ParameterDistribution("/Particle/Cylinder/Radius", gauss_distr1, nparticles, sigma_factor, limits) part_coll1 = ba.ParticleDistribution(cylinder1, par_distr1) # collection of particles #2 radius2 = 10.0 * nm height2 = radius2 sigma2 = radius2 * 0.02 cylinder_ff2 = ba.FormFactorCylinder(radius2, height2) cylinder2 = ba.Particle(m_particle, cylinder_ff2) gauss_distr2 = ba.DistributionGaussian(radius2, sigma2) par_distr2 = ba.ParameterDistribution("/Particle/Cylinder/Radius", gauss_distr2, nparticles, sigma_factor, limits) part_coll2 = ba.ParticleDistribution(cylinder2, par_distr2) # assembling the sample particle_layout = ba.ParticleLayout() particle_layout.addParticle(part_coll1, 0.95) particle_layout.addParticle(part_coll2, 0.05) vacuum_layer = ba.Layer(m_vacuum) vacuum_layer.addLayout(particle_layout) multi_layer = ba.MultiLayer() multi_layer.addLayer(vacuum_layer) return multi_layer
def getSample(): # Defining Materials material_2 = ba.HomogeneousMaterial("Si", 7.6e-06, 1.7e-07) material_1 = ba.HomogeneousMaterial("Air", 0.0, 0.0) # Defining Layers layer_1 = ba.Layer(material_1) layer_2 = ba.Layer(material_2) # Defining Form Factors formFactor_1 = ba.FormFactorCylinder(5.0 * nm, 5.0 * nm) # Defining Particles particle_1 = ba.Particle(material_2, formFactor_1) # Defining particles with parameter following a distribution distr_1 = ba.DistributionGaussian(5.0, 1.0) par_distr_1 = ba.ParameterDistribution("/Particle/Cylinder/Radius", distr_1, 10, 2.0) par_distr_1.linkParameter("/Particle/Cylinder/Height") particleDistribution_1 = ba.ParticleDistribution(particle_1, par_distr_1) # Defining Particle Layouts and adding Particles layout_1 = ba.ParticleLayout() layout_1.addParticle(particleDistribution_1, 1.0) layout_1.setTotalParticleSurfaceDensity(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 multilayer(self): """ Constructs the sample from current parameter values. """ # defining materials m_air = ba.HomogeneousMaterial("Air", 0.0, 0.0) m_Si = ba.HomogeneousMaterial("Si", 5.78164736e-6, 1.02294578e-7) m_Ag = ba.HomogeneousMaterial("Ag", 2.24749529E-5, 1.61528396E-6) m_PTFE = ba.HomogeneousMaterial("PTFE", 5.20508729E-6, 1.96944292E-8) m_HMDSO = ba.HomogeneousMaterial("HMDSO", 2.0888308E-6, 1.32605651E-8) # collection of particles with size distribution nparticles = 20 nfwhm = 2.0 sphere_ff = ba.FormFactorFullSphere(self.radius) sphere = ba.Particle(m_Ag, sphere_ff) position = ba.kvector_t(0 * ba.nm, 0 * ba.nm, -1.0 * self.hmdso_thickness) sphere.setPosition(position) ln_distr = ba.DistributionLogNormal(self.radius, self.sigma) par_distr = ba.ParameterDistribution( "/Particle/FullSphere/Radius", ln_distr, nparticles, nfwhm, ba.RealLimits.limited(0.0, self.hmdso_thickness / 2.0)) part_coll = ba.ParticleDistribution(sphere, par_distr) # interference function interference = ba.InterferenceFunctionRadialParaCrystal( self.distance, 1e6 * ba.nm) interference.setKappa(self.kappa) interference.setDomainSize(20000.0) pdf = ba.FTDistribution1DGauss(self.disorder) interference.setProbabilityDistribution(pdf) # assembling particle layout layout = ba.ParticleLayout() layout.addParticle(part_coll, 1.0) layout.setInterferenceFunction(interference) layout.setTotalParticleSurfaceDensity(1) # roughness r_ptfe = ba.LayerRoughness(2.3 * ba.nm, 0.3, 5.0 * ba.nm) r_hmdso = ba.LayerRoughness(1.1 * ba.nm, 0.3, 5.0 * ba.nm) # layers air_layer = ba.Layer(m_air) hmdso_layer = ba.Layer(m_HMDSO, self.hmdso_thickness) hmdso_layer.addLayout(layout) ptfe_layer = ba.Layer(m_PTFE, self.ptfe_thickness) substrate_layer = ba.Layer(m_Si) # assembling multilayer multi_layer = ba.MultiLayer() multi_layer.addLayer(air_layer) multi_layer.addLayerWithTopRoughness(hmdso_layer, r_hmdso) multi_layer.addLayerWithTopRoughness(ptfe_layer, r_ptfe) multi_layer.addLayer(substrate_layer) return multi_layer
def create_layout(self, particle_material): layout = ba.ParticleLayout() radius = 5.02 nparticles = 100 sigma = 0.3 gauss_distr = ba.DistributionGaussian(radius, sigma) # scale_param = math.sqrt(math.log((sigma / radius) ** 2 + 1.0)) # gauss_distr = ba.DistributionLogNormal(radius, scale_param) particle = ba.Particle(particle_material, ba.FormFactorFullSphere(radius)) sigma_factor = 2.0 par_distr = ba.ParameterDistribution("/Particle/FullSphere/Radius", gauss_distr, nparticles, sigma_factor) part_coll = ba.ParticleDistribution(particle, par_distr) layout.addParticle(part_coll, 1.0, ba.kvector_t(0, 0, -self.m_average_layer_thickness)) for i in range(0, 100): radius = npr.normal(5.0, 0.3) if radius < 4.0 or radius > 6.0: pass particle = ba.Particle(particle_material, ba.FormFactorFullSphere(radius)) zbot = -self.m_average_layer_thickness pos = random_gate(zbot, zbot + 50) layout.addParticle(particle, 0.05, ba.kvector_t(0, 0, pos)) layout.setTotalParticleSurfaceDensity(0.002) return layout
def create_diffuse_layout(particle_material, average_layer_thickness): """ Createss layout with mesocrystal collection. """ m_radius = 5.02 m_nparticles = 100 m_sigma = 0.5 m_diffuse_surface_density = 1e-2 layout = ba.ParticleLayout() distr = ba.DistributionGaussian(m_radius, m_sigma) # scale_param = math.sqrt(math.log((m_sigma / m_radius) ** 2 + 1.0)) # distr = ba.DistributionLogNormal(m_radius, scale_param) particle = ba.Particle(particle_material, ba.FormFactorFullSphere(m_radius)) sigma_factor = 3.0 par_distr = ba.ParameterDistribution("/Particle/FullSphere/Radius", distr, m_nparticles, sigma_factor) part_coll = ba.ParticleDistribution(particle, par_distr) layout.addParticle(part_coll, 1.0, ba.kvector_t(0, 0, -average_layer_thickness + 10)) layout.setTotalParticleSurfaceDensity(m_diffuse_surface_density) return layout
def get_vertical_lamellar(): mat_a = ba.HomogeneousMaterial("PTFE", 5.20508729E-6, 1.96944292E-8) mat_b = ba.HomogeneousMaterial("HMDSO", 2.0888308E-6, 1.32605651E-8) length = 30*nm width_a = 4*nm width_b = 8*nm height = 30*nm nstack = 5 stack = ba.ParticleComposition() for i in range(0, nstack): box_a = ba.Particle(mat_a, ba.FormFactorBox(length, width_a, height)) box_b = ba.Particle(mat_b, ba.FormFactorBox(length, width_b, height)) stack.addParticle(box_a, ba.kvector_t(0.0, i*(width_a+width_b), 0.0)) stack.addParticle(box_b, ba.kvector_t(0.0, (width_a + width_b)/2. + i*(width_a+width_b), 0.0)) stack.rotate(ba.RotationEuler(45.0*deg, 90.*deg, 0.0)) # Defining particles with parameter following a distribution gate = ba.DistributionGate(0.0*deg, 180.0*deg) par_distr = ba.ParameterDistribution("/ParticleComposition/EulerRotation/Alpha", gate, 60, 0.0) particles = ba.ParticleDistribution(stack, par_distr) stack.setPosition(0.0, 0.0, width_a/2.) return particles
def get_sample_rot_distr(): # create materials substrate_material = ba.HomogeneousMaterial("Substrate", 6.05878e-6, 6.94321e-11) particle_material = ba.HomogeneousMaterial("ParticleCore", -0.609e-6, 0.183e-6) layer_material = ba.HomogeneousMaterial("D2O", 1.85762e-5, 3.31309e-11) # create mesocrystal # lattice lat = create_hex_lattice(distance, length) # basis particle ff = ba.FormFactorCylinder(radius, length) particle = ba.Particle(particle_material, ff) # rotate cylinder to make it parallel to the substrate rotation = ba.RotationY(90.0 * ba.degree) particle.setRotation(rotation) basis = ba.ParticleComposition(particle) # mesocrystal total_height = nbr_layers * distance * np.sin(hex_angle) # using a Gaussian form factor as the overall shape of where the cylinders are meso_ff = ba.FormFactorGauss(meso_width, total_height) # assemble them into mesocrystal npc = ba.Crystal(basis, lat) dw_factor = 0.2 npc.setDWFactor(dw_factor) meso = ba.MesoCrystal(npc, meso_ff) # rotate mesocrystal rot_y = ba.RotationY(180.0 * ba.degree) meso.setRotation(rot_y) # turn upside down rot_z = ba.RotationZ(0.1 * ba.degree) meso.applyRotation(rot_z) # rotate around Z meso.setPosition(0.0, 0.0, 0.0) # add uniform distribution of the domain orientations rot_distr = ba.DistributionGate((90.0 - rz_range) * ba.degree, (90.0 + rz_range) * ba.degree) ang_distr = ba.ParameterDistribution("*MesoCrystal/EulerRotation/Gamma", rot_distr, rz_num) part_coll = ba.ParticleDistribution(meso, ang_distr) # Create multilayer multi_layer = ba.MultiLayer() d2o_layer = ba.Layer(layer_material) substrate_layer = ba.Layer(substrate_material) particle_layout = ba.ParticleLayout() particle_layout.addParticle(part_coll) d2o_layer.addLayout(particle_layout) # the sample is upside down multi_layer.addLayer(substrate_layer) multi_layer.addLayer(d2o_layer) return multi_layer
def create_diffuse_layout(self): layout = ba.ParticleLayout() radius = 5.0 nparticles = 100 sigma = 0.3 * radius gauss_distr = ba.DistributionGaussian(radius, sigma) particle = ba.Particle(self.m_adapted_particle_material, ba.FormFactorFullSphere(radius)) sigma_factor = 2.0 par_distr = ba.ParameterDistribution("/Particle/FullSphere/Radius", gauss_distr, nparticles, sigma_factor) part_coll = ba.ParticleDistribution(particle, par_distr) layout.addParticle( part_coll, 1.0, ba.kvector_t( 0, 0, -self.m_average_layer_thickness + self.m_meso_elevation)) layout.setTotalParticleSurfaceDensity(0.005) return layout
def get_sample(): """ Return a sample with cylinders on a substrate. The cylinders have a Gaussian size distribution. """ m_ambience = ba.HomogeneousMaterial("Air", 0.0, 0.0) m_particle = ba.HomogeneousMaterial("Particle", 6e-4, 2e-8) # cylindrical particle radius = 5 * nm height = radius cylinder_ff = ba.FormFactorCylinder(radius, height) cylinder = ba.Particle(m_particle, cylinder_ff) # collection of particles with size distribution nparticles = 100 sigma = 0.2 * radius gauss_distr = ba.DistributionGaussian(radius, sigma) sigma_factor = 2.0 par_distr = ba.ParameterDistribution("/Particle/Cylinder/Radius", gauss_distr, nparticles, sigma_factor) # by uncommenting the line below, the height of the cylinders # can be scaled proportionally to the radius: # par_distr.linkParameter("/Particle/Cylinder/Height") part_coll = ba.ParticleDistribution(cylinder, par_distr) # assembling the sample particle_layout = ba.ParticleLayout() particle_layout.addParticle(part_coll) air_layer = ba.Layer(m_ambience) air_layer.addLayout(particle_layout) multi_layer = ba.MultiLayer() multi_layer.addLayer(air_layer) return multi_layer
def get_sample(): """ Returns a sample """ # defining materials m_si = ba.MaterialBySLD("Si", sld_Si, sld_Si_im) m_d2o = ba.MaterialBySLD("D2O", sld_D2O, sld_D2O_im) m_core = ba.MaterialBySLD("Me3O5:D2O2", 2.0 * 1.0e-06, 0.0) m_shell = ba.MaterialBySLD("Me3O5:D2O", 3.9 * 1.0e-06, 0.0) # layer with particles # calculate average SLD Vcore = vol(core_radius, core_height) Vshell = vol(radius, height) - Vcore f_d2o = 0.7 f_core = (1.0 - f_d2o) / (1 + Vshell / Vcore) f_shell = (1.0 - f_d2o) / (1 + Vcore / Vshell) sld_mix = f_d2o * sld_D2O + f_shell * 3.9 * 1.0e-06 + f_core * 2.0 * 1.0e-06 m_mix = ba.MaterialBySLD("mix", sld_mix, 0.0) # fluctuation component ff_microgel = FormFactorMicrogel(b, xi, xiz) microgel = ba.Particle(m_core, ff_microgel) microgel_layout = ba.ParticleLayout() microgel_layout.addParticle(microgel, 1.0) # collection of particles ff = ba.FormFactorTruncatedSphere(radius=radius, height=height) ff_core = ba.FormFactorTruncatedSphere(radius=core_radius, height=core_height) transform = ba.RotationY(180.0 * deg) shell_particle = ba.Particle(m_shell, ff) core_particle = ba.Particle(m_core, ff_core) core_position = ba.kvector_t(0.0, 0.0, 0.0) particle = ba.ParticleCoreShell(shell_particle, core_particle, core_position) particle.setPosition(ba.kvector_t(0.0, 0.0, 0.0)) particle.setRotation(transform) nparticles = 2 # the larger is this number, the more slow will be the simulation. 10 is usually enough sigma = 0.2 * radius gauss_distr = ba.DistributionGaussian(radius, sigma) sigma_factor = 2.0 par_distr = ba.ParameterDistribution( "/ParticleCoreShell/Particle1/TruncatedSphere/Radius", gauss_distr, nparticles, sigma_factor, ba.RealLimits.lowerLimited(core_radius + 1.0)) par_distr.linkParameter( "/ParticleCoreShell/Particle1/TruncatedSphere/Height") par_distr.linkParameter( "/ParticleCoreShell/Particle0/TruncatedSphere/Height") par_distr.linkParameter( "/ParticleCoreShell/Particle0/TruncatedSphere/Radius") part_coll = ba.ParticleDistribution(particle, par_distr) microgel_layout.addParticle(part_coll, 1.2e-05) # interference can be neglected interference = ba.InterferenceFunctionNone() microgel_layout.setInterferenceFunction(interference) # describe layer roughness roughness = ba.LayerRoughness() roughness.setSigma(1.2 * ba.nm) roughness.setHurstParameter(0.8) roughness.setLatteralCorrLength(570.0 * ba.nm) # create layers d2o_layer = ba.Layer(m_d2o) mix_layer = ba.Layer(m_mix, 2.0 * height) mix_layer.addLayout(microgel_layout) si_layer = ba.Layer(m_si) multi_layer = ba.MultiLayer() multi_layer.addLayer(si_layer) multi_layer.addLayer(mix_layer) multi_layer.addLayerWithTopRoughness(d2o_layer, roughness) return multi_layer