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 get_sample(): """ Returns a sample with cylinders of two different sizes on a substrate. The cylinder positions are modelled in Local Monodisperse Approximation. """ m_ambience = ba.HomogeneousMaterial("Air", 0.0, 0.0) m_substrate = ba.HomogeneousMaterial("Substrate", 6e-6, 2e-8) m_particle = ba.HomogeneousMaterial("Particle", 6e-4, 2e-8) # cylindrical particle 1 radius1 = 5 * nm height1 = radius1 cylinder_ff1 = ba.FormFactorCylinder(radius1, height1) cylinder1 = ba.Particle(m_particle, cylinder_ff1) # cylindrical particle 2 radius2 = 8 * nm height2 = radius2 cylinder_ff2 = ba.FormFactorCylinder(radius2, height2) cylinder2 = ba.Particle(m_particle, cylinder_ff2) # interference function1 interference1 = ba.InterferenceFunctionRadialParaCrystal( 16.8 * nm, 1e3 * nm) pdf = ba.FTDistribution1DGauss(3 * nm) interference1.setProbabilityDistribution(pdf) # interference function2 interference2 = ba.InterferenceFunctionRadialParaCrystal( 22.8 * nm, 1e3 * nm) interference2.setProbabilityDistribution(pdf) # assembling the sample particle_layout1 = ba.ParticleLayout() particle_layout1.addParticle(cylinder1, 0.8) particle_layout1.setInterferenceFunction(interference1) particle_layout2 = ba.ParticleLayout() particle_layout2.addParticle(cylinder2, 0.2) particle_layout2.setInterferenceFunction(interference2) air_layer = ba.Layer(m_ambience) air_layer.addLayout(particle_layout1) air_layer.addLayout(particle_layout2) substrate_layer = ba.Layer(m_substrate) multi_layer = ba.MultiLayer() multi_layer.addLayer(air_layer) multi_layer.addLayer(substrate_layer) return multi_layer
def create_meso(self): ff_meso = ba.FormFactorCylinder(self.m_meso_radius, self.m_meso_height) lattice = self.create_lattice(self.m_lattice_length_a, self.m_lattice_length_c) basis = self.create_basis(self.particle_material, lattice, self.m_nanoparticle_radius, self.m_sigma_nanoparticle_radius, self.m_nparticles) npc = ba.Crystal(basis, lattice) dw_factor = self.particle_pos_sigma * self.particle_pos_sigma npc.setPositionVariance(dw_factor) result = ba.MesoCrystal(npc, ff_meso) if self.m_rotation_z != 0.0: rotZ = ba.RotationZ(self.m_rotation_z * deg) result.setRotation(rotZ) if self.m_rotation_x != 0.0: rotX = ba.RotationX(self.m_rotation_x * deg) result.rotate(rotX) return result
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_sample(radius=5.0 * nm, height=5.0 * nm, lattice_constant=10.0 * nm): """ Returns a sample with cylinders on a substrate, forming a rectangular lattice. """ m_air = ba.HomogeneousMaterial("Air", 0.0, 0.0) m_substrate = ba.HomogeneousMaterial("Substrate", 6e-6, 2e-8) m_particle = ba.HomogeneousMaterial("Particle", 6e-4, 2e-8) ff = ba.FormFactorCylinder(radius, height) cylinder = ba.Particle(m_particle, ff) particle_layout = ba.ParticleLayout() particle_layout.addParticle(cylinder) interference = ba.InterferenceFunction2DLattice(lattice_constant, lattice_constant, 90.0 * deg) pdf = ba.FTDecayFunction2DCauchy(50 * nm, 50 * nm) interference.setDecayFunction(pdf) particle_layout.setInterferenceFunction(interference) air_layer = ba.Layer(m_air) air_layer.addLayout(particle_layout) substrate_layer = ba.Layer(m_substrate, 0) multi_layer = ba.MultiLayer() multi_layer.addLayer(air_layer) multi_layer.addLayer(substrate_layer) return multi_layer
def test_parameterPoolAccess(self): """ Checks values in particle's parameter pool """ ff = ba.FormFactorCylinder(5 * nm, 6 * nm) particle = ba.Particle(ba.HomogeneousMaterial("Air", 0.0, 0.0), ff) particle.setAbundance(1.0) particle.setPosition(2.0, 3.0, 4.0) # print(particle.parametersToString()) # print(particle.treeToString()) pool = particle.parameterPool() self.assertEqual(pool.size(), 4) self.assertEqual(pool.parameterNames(), ('Abundance', 'PositionX', 'PositionY', 'PositionZ')) expected = { 'Abundance': 1.0, 'PositionX': 2.0, 'PositionY': 3.0, 'PositionZ': 4.0 } for par in pool: print(par.value(), par.getName(), par.limits().toString()) self.assertEqual(par.value(), expected[par.getName()])
def get_sample(): """ Returns a sample with cylinders on a substrate, forming a 2D lattice with different disorder rotated lattice """ m_ambience = ba.HomogeneousMaterial("Air", 0.0, 0.0) m_substrate = ba.HomogeneousMaterial("Substrate", 6e-6, 2e-8) m_particle = ba.HomogeneousMaterial("Particle", 6e-4, 2e-8) air_layer = ba.Layer(m_ambience) substrate_layer = ba.Layer(m_substrate) p_interference_function = \ ba.InterferenceFunction2DLattice.createSquare(25.0*nm) pdf = ba.FTDecayFunction2DCauchy(300.0 * nm / 2.0 / numpy.pi, 100.0 * nm / 2.0 / numpy.pi) p_interference_function.setDecayFunction(pdf) particle_layout = ba.ParticleLayout() ff_cyl = ba.FormFactorCylinder(3.0 * nm, 3.0 * nm) position = ba.kvector_t(0.0, 0.0, 0.0) cylinder = ba.Particle(m_particle, ff_cyl.clone()) cylinder.setPosition(position) particle_layout.addParticle(cylinder, 1.0) particle_layout.setInterferenceFunction(p_interference_function) air_layer.addLayout(particle_layout) multi_layer = ba.MultiLayer() multi_layer.addLayer(air_layer) multi_layer.addLayer(substrate_layer) return multi_layer
def get_sample(params): """ Returns a sample with uncorrelated cylinders and prisms on a substrate. """ cylinder_height = params["cylinder_height"] cylinder_radius = params["cylinder_radius"] prism_height = params["prism_height"] prism_base_edge = params["prism_base_edge"] # defining materials m_vacuum = ba.HomogeneousMaterial("Vacuum", 0.0, 0.0) m_substrate = ba.HomogeneousMaterial("Substrate", 6e-6, 2e-8) m_particle = ba.HomogeneousMaterial("Particle", 6e-4, 2e-8) # collection of particles cylinder_ff = ba.FormFactorCylinder(cylinder_radius, cylinder_height) cylinder = ba.Particle(m_particle, cylinder_ff) prism_ff = ba.FormFactorPrism3(prism_base_edge, prism_height) prism = ba.Particle(m_particle, prism_ff) layout = ba.ParticleLayout() layout.addParticle(cylinder, 0.5) layout.addParticle(prism, 0.5) interference = ba.InterferenceFunctionNone() layout.setInterferenceFunction(interference) # vacuum layer with particles and substrate form multi layer vacuum_layer = ba.Layer(m_vacuum) vacuum_layer.addLayout(layout) substrate_layer = ba.Layer(m_substrate, 0) multi_layer = ba.MultiLayer() multi_layer.addLayer(vacuum_layer) multi_layer.addLayer(substrate_layer) return multi_layer
def get_sample(params): """ Returns a sample with uncorrelated cylinders and pyramids on a substrate. """ radius = params["radius"] height = params["height"] m_vacuum = ba.HomogeneousMaterial("Vacuum", 0.0, 0.0) m_substrate = ba.HomogeneousMaterial("Substrate", 6e-6, 2e-8) m_particle = ba.HomogeneousMaterial("Particle", 6e-4, 2e-8) cylinder_ff = ba.FormFactorCylinder(radius, height) cylinder = ba.Particle(m_particle, cylinder_ff) layout = ba.ParticleLayout() layout.addParticle(cylinder) vacuum_layer = ba.Layer(m_vacuum) vacuum_layer.addLayout(layout) substrate_layer = ba.Layer(m_substrate, 0) multi_layer = ba.MultiLayer() multi_layer.addLayer(vacuum_layer) multi_layer.addLayer(substrate_layer) return multi_layer
def get_sample(): """ Returns a sample with uncorrelated cylinders and prisms on a substrate. """ # defining materials m_vacuum = ba.HomogeneousMaterial("Vacuum", 0.0, 0.0) m_substrate = ba.HomogeneousMaterial("Substrate", 6e-6, 2e-8) m_particle = ba.HomogeneousMaterial("Particle", 6e-4, 2e-8) # collection of particles cylinder_ff = ba.FormFactorCylinder(5 * nm, 5 * nm) cylinder = ba.Particle(m_particle, cylinder_ff) prism_ff = ba.FormFactorPrism3(10 * nm, 5 * nm) prism = ba.Particle(m_particle, prism_ff) particle_layout = ba.ParticleLayout() particle_layout.addParticle(cylinder, 0.5) particle_layout.addParticle(prism, 0.5) interference = ba.InterferenceFunctionNone() particle_layout.setInterferenceFunction(interference) # vacuum layer with particles and substrate form multi layer vacuum_layer = ba.Layer(m_vacuum) vacuum_layer.addLayout(particle_layout) substrate_layer = ba.Layer(m_substrate) multi_layer = ba.MultiLayer() multi_layer.addLayer(vacuum_layer) multi_layer.addLayer(substrate_layer) print(multi_layer.treeToString()) return multi_layer
def get_sample(params): """ Build the sample representing cylinders on top of substrate without interference. """ radius = params["radius"] height = params["height"] m_vacuum = ba.HomogeneousMaterial("Vacuum", 0.0, 0.0) m_substrate = ba.HomogeneousMaterial("Substrate", 6e-6, 2e-8) m_particle = ba.HomogeneousMaterial("Particle", 6e-4, 2e-8) cylinder_ff = ba.FormFactorCylinder(radius, height) cylinder = ba.Particle(m_particle, cylinder_ff) layout = ba.ParticleLayout() layout.addParticle(cylinder) vacuum_layer = ba.Layer(m_vacuum) vacuum_layer.addLayout(layout) substrate_layer = ba.Layer(m_substrate, 0) multi_layer = ba.MultiLayer() multi_layer.addLayer(vacuum_layer) multi_layer.addLayer(substrate_layer) return multi_layer
def get_sample(): """ Returns a sample with uncorrelated cylinders and prisms on a substrate. Parameter set is fixed. """ # defining materials m_air = ba.HomogeneousMaterial("Air", 0.0, 0.0) m_substrate = ba.HomogeneousMaterial("Substrate", 6e-6, 2e-8) m_particle = ba.HomogeneousMaterial("Particle", 6e-4, 2e-8) # collection of particles cylinder_ff = ba.FormFactorCylinder(5 * nm, 5 * nm) cylinder = ba.Particle(m_particle, cylinder_ff) prism_ff = ba.FormFactorPrism3(5 * nm, 5 * nm) prism = ba.Particle(m_particle, prism_ff) layout = ba.ParticleLayout() layout.addParticle(cylinder, 0.5) layout.addParticle(prism, 0.5) interference = ba.InterferenceFunctionNone() layout.setInterferenceFunction(interference) # air layer with particles and substrate form multi layer air_layer = ba.Layer(m_air) air_layer.addLayout(layout) substrate_layer = ba.Layer(m_substrate, 0) multi_layer = ba.MultiLayer() multi_layer.addLayer(air_layer) multi_layer.addLayer(substrate_layer) return multi_layer
def create_sample(): # create materials magnetic_field = ba.kvector_t(1.0, 1.0, 1.0) substr_field = ba.kvector_t(0.0, 1.0, 0.0) particle_material = ba.HomogeneousMagneticMaterial("particle", 2e-5, 4e-7, magnetic_field) air_material = ba.HomogeneousMaterial("Air", 0.0, 0.0) substrate_material = ba.HomogeneousMagneticMaterial( "Substrate", 7e-6, 1.8e-7, substr_field) # Create multilayer particle_layout = ba.ParticleLayout() cylinder_ff = ba.FormFactorCylinder(5 * nm, 5 * nm) cylinder = ba.Particle(particle_material, cylinder_ff) particle_layout.addParticle(cylinder) air_layer = ba.Layer() air_layer.setMaterial(air_material) air_layer.addLayout(particle_layout) substrate_layer = ba.Layer() substrate_layer.setMaterial(substrate_material) multi_layer = ba.MultiLayer() multi_layer.addLayer(air_layer) multi_layer.addLayer(substrate_layer) return multi_layer
def get_sample(): """ Returns a sample with uncorrelated cylinders and prisms on a substrate. Parameter set is fixed. """ # defining materials m_air = ba.HomogeneousMaterial("Air", 0.0, 0.0) m_substrate = ba.HomogeneousMaterial("Substrate", 6e-6, 2e-8) m_particle = ba.HomogeneousMaterial("Particle", 6e-4, 2e-8) # collection of particles cylinder_ff = ba.FormFactorCylinder(5*nm, 5*nm) cylinder = ba.Particle(m_particle, cylinder_ff) prism_ff = ba.FormFactorPrism3(5*nm, 5*nm) prism = ba.Particle(m_particle, prism_ff) particle_layout = ba.ParticleLayout() particle_layout.addParticle(cylinder, 0.5) particle_layout.addParticle(prism, 0.5) # interference = ba.InterferenceFunctionRadialParaCrystal(20.0*nm, 1e3*nm) # pdf = ba.FTDistribution1DGauss(7 * nm) # interference.setProbabilityDistribution(pdf) # particle_layout.addInterferenceFunction(interference) # air layer with particles and substrate form multi layer air_layer = ba.Layer(m_air) air_layer.addLayout(particle_layout) substrate_layer = ba.Layer(m_substrate, 0) multi_layer = ba.MultiLayer() multi_layer.addLayer(air_layer) multi_layer.addLayer(substrate_layer) return multi_layer
def get_sample(): """ Returns a sample with cylinders on a substrate, forming a 2D square lattice. """ # defining materials m_vacuum = ba.HomogeneousMaterial("Vacuum", 0.0, 0.0) m_substrate = ba.HomogeneousMaterial("Substrate", 6e-6, 2e-8) m_particle = ba.HomogeneousMaterial("Particle", 6e-4, 2e-8) # collection of particles interference = ba.InterferenceFunction2DLattice.createSquare( 25.0 * nm, 0 * deg) pdf = ba.FTDecayFunction2DCauchy(300.0 * nm / 2.0 / numpy.pi, 100.0 * nm / 2.0 / numpy.pi, 0) interference.setDecayFunction(pdf) cylinder_ff = ba.FormFactorCylinder(3. * nm, 3. * nm) cylinder = ba.Particle(m_particle, cylinder_ff) particle_layout = ba.ParticleLayout() particle_layout.addParticle(cylinder) particle_layout.setInterferenceFunction(interference) # assembling the sample vacuum_layer = ba.Layer(m_vacuum) vacuum_layer.addLayout(particle_layout) substrate_layer = ba.Layer(m_substrate) multi_layer = ba.MultiLayer() multi_layer.addLayer(vacuum_layer) multi_layer.addLayer(substrate_layer) print(multi_layer.parametersToString()) print(multi_layer.treeToString()) return multi_layer
def get_sample(): """ Returns a sample with cylinders on a substrate, forming a 2D square lattice. """ # defining materials m_ambience = ba.HomogeneousMaterial("Air", 0.0, 0.0) m_substrate = ba.HomogeneousMaterial("Substrate", 6e-6, 2e-8) m_particle = ba.HomogeneousMaterial("Particle", 6e-4, 2e-8) # collection of particles interference = ba.InterferenceFunctionFinite2DLattice.createSquare( 25.0 * nm, 0.0, 40, 40) interference.setPositionVariance(1.0) cylinder_ff = ba.FormFactorCylinder(3. * nm, 3. * nm) cylinder = ba.Particle(m_particle, cylinder_ff) particle_layout = ba.ParticleLayout() particle_layout.addParticle(cylinder) particle_layout.setInterferenceFunction(interference) # assembling the sample air_layer = ba.Layer(m_ambience) air_layer.addLayout(particle_layout) substrate_layer = ba.Layer(m_substrate) multi_layer = ba.MultiLayer() multi_layer.addLayer(air_layer) multi_layer.addLayer(substrate_layer) print(multi_layer.parametersToString()) print(multi_layer.treeToString()) return multi_layer
def get_sample(): """ Returns a sample with cylinders on a substrate, forming a 2D paracrystal """ m_ambience = ba.HomogeneousMaterial("Air", 0.0, 0.0) m_substrate = ba.HomogeneousMaterial("Substrate", 6e-6, 2e-8) m_particle = ba.HomogeneousMaterial("Particle", 6e-4, 2e-8) # collection of particles cylinder_ff = ba.FormFactorCylinder(4 * nm, 5 * nm) cylinder = ba.Particle(m_particle, cylinder_ff) interference = ba.InterferenceFunction2DParaCrystal.createSquare( 10.0 * nm, 0.0, 20.0 * micrometer, 20.0 * micrometer) pdf = ba.FTDistribution2DCauchy(1.0 * nm, 1.0 * nm) interference.setProbabilityDistributions(pdf, pdf) particle_layout = ba.ParticleLayout() particle_layout.addParticle(cylinder, 1.0) particle_layout.setInterferenceFunction(interference) # assembling the sample air_layer = ba.Layer(m_ambience) air_layer.addLayout(particle_layout) substrate_layer = ba.Layer(m_substrate) multi_layer = ba.MultiLayer() multi_layer.addLayer(air_layer) multi_layer.addLayer(substrate_layer) print(multi_layer.parametersToString()) print(multi_layer.treeToString()) 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 runSimulation(): # defining materials mAmbience = ba.HomogeneousMaterial("Air", 0.0, 0.0) mSubstrate = ba.HomogeneousMaterial("Substrate", 6e-6, 2e-8) magnetic_field = ba.kvector_t(0, 0, 0) magParticle = ba.HomogeneousMaterial("magParticle", 6e-4, 2e-8, magnetic_field ) # collection of particles cylinder_ff = ba.FormFactorCylinder(5*nanometer, 5*nanometer) cylinder = ba.Particle(magParticle, cylinder_ff) particle_layout = ba.ParticleLayout() particle_layout.addParticle(cylinder, 1.0) interference = ba.InterferenceFunctionNone() particle_layout.setInterferenceFunction(interference) # air layer with particles and substrate form multi layer air_layer = ba.Layer(mAmbience) air_layer.addLayout(particle_layout) substrate_layer = ba.Layer(mSubstrate, 0) multi_layer = ba.MultiLayer() multi_layer.addLayer(air_layer) multi_layer.addLayer(substrate_layer) # build and run experiment simulation = ba.GISASSimulation() simulation.setDetectorParameters(100, 0*degree, 2.0*degree, 100, 0.0*degree, 2.0*degree) simulation.setBeamParameters(1.0*angstrom, 0.2*degree, 0.0*degree) simulation.setSample(multi_layer) simulation.setBeamIntensity(1e2) simulation.runSimulation() ## intensity data return simulation.result()
def get_sample(): """ Returns a sample with cylinders on a substrate that form a radial paracrystal. """ # defining materials m_ambience = ba.HomogeneousMaterial("Air", 0.0, 0.0) m_substrate = ba.HomogeneousMaterial("Substrate", 6e-6, 2e-8) m_particle = ba.HomogeneousMaterial("Particle", 6e-4, 2e-8) # collection of particles cylinder_ff = ba.FormFactorCylinder(5*nm, 5*nm) cylinder = ba.Particle(m_particle, cylinder_ff) interference = ba.InterferenceFunctionRadialParaCrystal( 20.0*nm, 1e3*nm) pdf = ba.FTDistribution1DGauss(7 * nm) interference.setProbabilityDistribution(pdf) particle_layout = ba.ParticleLayout() particle_layout.addParticle(cylinder, 1.0) particle_layout.setInterferenceFunction(interference) # assembling the sample air_layer = ba.Layer(m_ambience) air_layer.addLayout(particle_layout) substrate_layer = ba.Layer(m_substrate) multi_layer = ba.MultiLayer() multi_layer.addLayer(air_layer) multi_layer.addLayer(substrate_layer) # print(multi_layer.treeToString()) return multi_layer
def get_sample(): """ Returns a sample with cylinders on a substrate, forming a rotated 2D lattice """ # defining materials m_ambience = ba.HomogeneousMaterial("Air", 0.0, 0.0) m_substrate = ba.HomogeneousMaterial("Substrate", 6e-6, 2e-8) m_particle = ba.HomogeneousMaterial("Particle", 6e-4, 2e-8) # collection of particles interference = ba.InterferenceFunction2DLattice.createSquare( 25.0*nm, 30.0*deg) pdf = ba.FTDecayFunction2DCauchy( 300.0*nm/2.0/numpy.pi, 100.0*nm/2.0/numpy.pi) pdf.setGamma(30.0*deg) interference.setDecayFunction(pdf) cylinder_ff = ba.FormFactorCylinder(3.*nm, 3.*nm) cylinder = ba.Particle(m_particle, cylinder_ff) particle_layout = ba.ParticleLayout() particle_layout.addParticle(cylinder) particle_layout.setInterferenceFunction(interference) # assembling the sample air_layer = ba.Layer(m_ambience) air_layer.addLayout(particle_layout) substrate_layer = ba.Layer(m_substrate) multi_layer = ba.MultiLayer() multi_layer.addLayer(air_layer) multi_layer.addLayer(substrate_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) # cylindrical particles with bivariate size distribution radius = 5 * nm # mean radius height = radius # mean height nparticles = 10 nfwhm = 2.0 sigma = 0.2 * radius # sx = sy = sigma distr = BivariateGaussian(mx=radius, my=height, sx=sigma, sy=sigma) params = distr.gen_parameters(nparticles, nfwhm) layout_1 = ba.ParticleLayout() for p in params: cylinder_ff = ba.FormFactorCylinder(p['radius'], p['height']) cylinder = ba.Particle(material_2, cylinder_ff) layout_1.addParticle(cylinder, p['abundance']) # 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 test_parameterTreeModify(self): """ Modifies values of particle's parameter tree. """ ff = ba.FormFactorCylinder(5 * nm, 6 * nm) particle = ba.Particle(ba.HomogeneousMaterial("Air", 0.0, 0.0), ff) particle.setAbundance(1.0) particle.setPosition(2.0, 3.0, 4.0) # print(particle.parametersToString()) # print(particle.treeToString()) pool = particle.createParameterTree() pool.setParameterValue('/Particle/Abundance', 10.0) pool[1].setValue(20.0) # PositionX pool.parameter('/Particle/PositionY').setValue(30.0) pool.setMatchedParametersValue('*Cylinder*', 50.0) expected = { '/Particle/Abundance': 10.0, '/Particle/PositionX': 20.0, '/Particle/PositionY': 30.0, '/Particle/PositionZ': 4.0, '/Particle/Cylinder/Radius': 50.0, '/Particle/Cylinder/Height': 50.0 } for par in pool: self.assertEqual(par.value(), expected[par.getName()])
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 get_composition(top_material, bottom_material, top_height=4.0, bottom_height=10.0): """ Returns cylindrical particle made of two different materials. """ cylinder_radius = 10 * nm topPart = ba.Particle(top_material, ba.FormFactorCylinder(cylinder_radius, top_height)) bottomPart = ba.Particle( bottom_material, ba.FormFactorCylinder(cylinder_radius, bottom_height)) result = ba.ParticleComposition() result.addParticle(topPart, ba.kvector_t(0.0, 0.0, bottom_height)) result.addParticle(bottomPart) return result
def get_sample(): """ Returns a sample with cylinders of two different sizes on a substrate. The cylinder positions are modelled in Size-Spacing Coupling Approximation. """ m_vacuum = ba.HomogeneousMaterial("Vacuum", 0.0, 0.0) m_substrate = ba.HomogeneousMaterial("Substrate", 6e-6, 2e-8) m_particle = ba.HomogeneousMaterial("Particle", 6e-4, 2e-8) # cylindrical particle 1 radius1 = 5 * nm height1 = radius1 cylinder_ff1 = ba.FormFactorCylinder(radius1, height1) cylinder1 = ba.Particle(m_particle, cylinder_ff1) # cylindrical particle 2 radius2 = 8 * nm height2 = radius2 cylinder_ff2 = ba.FormFactorCylinder(radius2, height2) cylinder2 = ba.Particle(m_particle, cylinder_ff2) # interference function interference = ba.InterferenceFunctionRadialParaCrystal( 18.0 * nm, 1e3 * nm) pdf = ba.FTDistribution1DGauss(3 * nm) interference.setProbabilityDistribution(pdf) interference.setKappa(1.0) # assembling the sample particle_layout = ba.ParticleLayout() particle_layout.addParticle(cylinder1, 0.8) particle_layout.addParticle(cylinder2, 0.2) particle_layout.setInterferenceFunction(interference) vacuum_layer = ba.Layer(m_vacuum) vacuum_layer.addLayout(particle_layout) substrate_layer = ba.Layer(m_substrate) multi_layer = ba.MultiLayer() multi_layer.addLayer(vacuum_layer) multi_layer.addLayer(substrate_layer) return multi_layer
def test_parameterModify(self): """ Modification of particle's parameters without intermediate access to parameter pool """ ff = ba.FormFactorCylinder(5 * nm, 6 * nm) particle = ba.Particle(ba.HomogeneousMaterial("Air", 0.0, 0.0), ff) particle.setAbundance(1.0) particle.setPosition(2.0, 3.0, 4.0) particle.setParameterValue('/Particle/Abundance', 10.0) particle.setParameterValue('PositionZ', 40.0) particle.setParameterValue('*Cylinder*', 50.0) self.assertEqual(particle.abundance(), 10.0) self.assertEqual(particle.position().z(), 40.0)
def get_sample(): """ Returns a sample with cylinders in a homogeneous environment ("air"), implying a simulation in plain Born approximation. """ # defining materials m_ambience = ba.HomogeneousMaterial("Air", 0.0, 0.0) m_particle = ba.HomogeneousMaterial("Particle", 6e-4, 2e-8) # collection of particles cylinder_ff = ba.FormFactorCylinder(5 * nm, 5 * nm) cylinder = ba.Particle(m_particle, cylinder_ff) particle_layout = ba.ParticleLayout() particle_layout.addParticle(cylinder, 1.0) 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(radius=5.0 * nm, height=10.0 * nm): """ Build the sample representing cylinders on top of substrate without interference. """ m_air = ba.HomogeneousMaterial("Air", 0.0, 0.0) m_substrate = ba.HomogeneousMaterial("Substrate", 6e-6, 2e-8) m_particle = ba.HomogeneousMaterial("Particle", 6e-4, 2e-8) cylinder_ff = ba.FormFactorCylinder(radius, height) cylinder = ba.Particle(m_particle, cylinder_ff) particle_layout = ba.ParticleLayout() particle_layout.addParticle(cylinder) air_layer = ba.Layer(m_air) air_layer.addLayout(particle_layout) substrate_layer = ba.Layer(m_substrate, 0) multi_layer = ba.MultiLayer() multi_layer.addLayer(air_layer) multi_layer.addLayer(substrate_layer) return multi_layer
def get_sample(radius=5.0 * nm, height=10.0 * nm): """ Returns a sample with uncorrelated cylinders on a substrate. """ m_air = ba.HomogeneousMaterial("Air", 0.0, 0.0) m_substrate = ba.HomogeneousMaterial("Substrate", 6e-6, 2e-8) m_particle = ba.HomogeneousMaterial("Particle", 6e-4, 2e-8) cylinder_ff = ba.FormFactorCylinder(radius, height) cylinder = ba.Particle(m_particle, cylinder_ff) particle_layout = ba.ParticleLayout() particle_layout.addParticle(cylinder) air_layer = ba.Layer(m_air) air_layer.addLayout(particle_layout) substrate_layer = ba.Layer(m_substrate, 0) multi_layer = ba.MultiLayer() multi_layer.addLayer(air_layer) multi_layer.addLayer(substrate_layer) return multi_layer