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
