def testSphericalLacuneInSubstrate(self):
"""
Similar to previous. Truncated sphere and sphere are made of air material.
From scattering point of view, both cases should look like an air lacune in substrate.
"""
sphere_radius = 10.0
sphere_shift = 4.0 # shift beneath interface in absolute units
# Sphere truncated from top. Intended to go below interface.
truncatedSphere = ba.Particle(
mAmbience,
ba.FormFactorTruncatedSphere(sphere_radius, sphere_radius * 2,
sphere_radius * 2 - sphere_shift))
truncatedSphere.setPosition(0, 0, -sphere_shift)
reference = self.get_result(truncatedSphere)
# sphere crossing interface to look like truncated sphere above
sphere = ba.Particle(mAmbience, ba.FormFactorFullSphere(sphere_radius))
sphere.setPosition(0, 0, -sphere_shift)
data = self.get_result(sphere)
diff = ba.RelativeDifference(data, reference)
print(diff)
self.assertLess(diff, 1e-10)
def testSpheresCrossingInterface(self):
"""
Compares two simulation intended to provide identical results.
Simulation #1: full sphere inserted in air layer to cross interface
Simulation #2: full sphere inserted in substrate layer to cross interface
Both spheres are made of same material.
"""
mParticle = ba.HomogeneousMaterial("Ag", 1.245e-5, 5.419e-7)
sphere_radius = 10.0
sphere_shift = 4.0 # shift beneath interface in absolute units
# Sphere intended for air layer and crossing interface
sphere1 = ba.Particle(mParticle,
ba.FormFactorFullSphere(sphere_radius))
sphere1.setPosition(0, 0, -sphere_shift)
reference = self.get_result(particle_to_air=sphere1)
# Sphere intended for substrate layer and crossing interface
sphere2 = ba.Particle(mParticle,
ba.FormFactorFullSphere(sphere_radius))
sphere2.setPosition(0, 0, -sphere_shift)
data = self.get_result(particle_to_substrate=sphere2)
diff = ba.RelativeDifference(data, reference)
print(diff)
self.assertLess(diff, 1e-10)
def testSphericalCupOnTopOfSubstrate(self):
"""
Compares two simulation intended to provide identical results.
Simulation #1: truncated sphere on top of substrate.
Simulation #2: spherical particle crossing the interface.
Both particles are made of same material as substrate. From scattering point of view,
both cases should look like a truncated sphere on top of substrate.
"""
sphere_radius = 10.0
sphere_shift = 4.0 # shift beneath interface in absolute units
# truncated sphere on top of substrate with height 16nm
truncatedSphere = ba.Particle(
mSubstrate,
ba.FormFactorTruncatedSphere(sphere_radius,
sphere_radius * 2 - sphere_shift))
reference = self.get_result(truncatedSphere)
# sphere crossing interface to look like truncated sphere above
sphere = ba.Particle(mSubstrate,
ba.FormFactorFullSphere(sphere_radius))
sphere.setPosition(0, 0, -sphere_shift)
data = self.get_result(sphere)
diff = ba.RelativeDifference(data, reference)
print(diff)
self.assertLess(diff, 1e-10)
def testBoxTransform(self):
"""
Reference box of (10,50,20) size is compared against the box (50,20,10) with two rotations applied to get
reference one
"""
mParticle = ba.HomogeneousMaterial("Ag", 1.245e-5, 5.419e-7)
# reference box
length = 10
width = 50
height = 20
box = ba.Particle(mParticle, ba.FormFactorBox(length, width, height))
box.setPosition(kvector_t(0, 0, -layer_thickness/2 - height/2))
reference_data = self.get_result(box)
#IntensityDataIOFactory.writeIntensityData(reference_data, "ref_TransformBox.int")
# second box
length = 50
width = 20
height = 10
box = ba.Particle(mParticle, ba.FormFactorBox(length, width, height))
box.setRotation(ba.RotationZ(90*deg))
box.rotate(ba.RotationY(90*deg))
box.setPosition(kvector_t(0, 0, -layer_thickness/2))
data = self.get_result(box)
diff = ba.RelativeDifference(data, reference_data)
print(diff)
self.assertLess(diff, 1e-10)
def testSphericalCupOnTopOfSubstrate(self):
"""
Compares two simulation intended to provide identical results.
Simulation #1: truncated sphere on top of substrate.
Simulation #2: spherical particle composition crossing the interface.
Bottom part of composition is made from substrate material.
both cases should look like a truncated sphere on top of substrate.
"""
# truncated sphere on top of substrate with height 16nm
truncatedSphere = ba.Particle(
mParticle,
ba.FormFactorTruncatedSphere(sphere_radius, sphere_radius * 2 -
bottom_cup_height))
reference = self.get_intensity_data(truncatedSphere)
# Particle composition, top part made of same material, as particle. Bottom part made of same material as substrate.
composition = self.get_composition(mParticle, mSubstrate)
composition_shift = bottom_cup_height
composition.setPosition(0, 0, -composition_shift)
data = self.get_intensity_data(composition)
diff = ba.getRelativeDifference(data, reference)
print(diff)
self.assertLess(diff, 1e-10)
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.runSimulation()
## intensity data
return simulation.getIntensityData()
def get_composition_v2(self, top_material, bottom_material):
"""
Returns particle composition representing sphere made of two different materials.
Alternative to previous method.
Rotation is used to get bottom part
"""
topCup = ba.Particle(
top_material,
ba.FormFactorTruncatedSphere(sphere_radius, sphere_radius * 2 -
bottom_cup_height))
bottomCup = ba.Particle(
bottom_material,
ba.FormFactorTruncatedSphere(sphere_radius, bottom_cup_height))
bottomCup.setRotation(ba.RotationX(180 * deg))
# origin of resulting sphere will be at the bottom
result = ba.ParticleComposition()
result.addParticle(topCup, kvector_t(0.0, 0.0, bottom_cup_height))
result.addParticle(bottomCup, kvector_t(0.0, 0.0, bottom_cup_height))
return result
def get_composition(self, top_material, bottom_material):
"""
Returns particle composition representing sphere made of two different materials.
Origin of new object is at the bottom of resulting sphere.
"""
topCup = ba.Particle(
top_material,
ba.FormFactorTruncatedSphere(sphere_radius, sphere_radius * 2 -
bottom_cup_height))
bottomCup = ba.Particle(
bottom_material,
ba.FormFactorTruncatedSphere(sphere_radius, sphere_radius * 2,
sphere_radius * 2 -
bottom_cup_height))
# origin of resulting sphere will be at the bottom
result = ba.ParticleComposition()
result.addParticle(topCup, kvector_t(0.0, 0.0, bottom_cup_height))
result.addParticle(bottomCup, kvector_t(0.0, 0.0, 0.0))
return result
def testComposition(self):
"""
Compares two simulation intended to provide identical results.
Simulation #1: spherical particle on top of substrate
Simulation #2: spherical composition on top of substrate, where top and bottom are made of same material
"""
# spherical particle
sphere = ba.Particle(mParticle, ba.FormFactorFullSphere(sphere_radius))
reference = self.get_intensity_data(sphere)
# spherical composition
composition = self.get_composition(mParticle, mParticle)
data = self.get_intensity_data(composition)
diff = ba.getRelativeDifference(data, reference)
print(diff)
self.assertLess(diff, 1e-10)
def testSlicedComposition(self):
"""
Compares two simulation intended to provide identical results.
Simulation #1: spherical particle on top of substrate
Simulation #2: spherical composition on top of substrate, where top and bottom are made of same material
Both particles are inserted in air layer with shift to go below interface
"""
shift = 3 * nm
# spherical particle
sphere = ba.Particle(mParticle, ba.FormFactorFullSphere(sphere_radius))
sphere.setPosition(0, 0, -shift)
reference = self.get_intensity_data(sphere)
# spherical composition
composition = self.get_composition(mParticle, mParticle)
composition.setPosition(0, 0, -shift)
data = self.get_intensity_data(composition)
diff = ba.getRelativeDifference(data, reference)
print(diff)
self.assertLess(diff, 1e-10)