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
