def simsmuthi(ii, lams, nkdata, fname, rad, subri):
wl = lams[ii]
parri = nkdata[ii]
angles = np.linspace(0, np.pi, 181)
z0 = -rad
pos = LoadPosFile(fname, cc, rad, z0)
par_list = PrepareIdenticalParticles(positions=pos,
ref_ind=parri,
radius=rad)
coord.set_default_k_parallel(wl, neff_resolution=5e-3, neff_max=subri + 1)
two_layers = smuthi.layers.LayerSystem(thicknesses=[0, 0],
refractive_indices=[1, subri])
plane_wave = smuthi.initial_field.PlaneWave(
vacuum_wavelength=wl,
polar_angle=0, # from top
azimuthal_angle=0,
polarization=0) # 0=TE 1=TM
if len(par_list) == 1:
simulation = smuthi.simulation.Simulation(layer_system=two_layers,
particle_list=par_list,
initial_field=plane_wave,
solver_type='gmres')
else:
simulation = smuthi.simulation.Simulation(
layer_system=two_layers,
particle_list=par_list,
initial_field=plane_wave,
solver_type='KCSolver',
store_coupling_matrix=False,
coupling_matrix_lookup_resolution=3)
simulation.run()
# evaluate differential scattering cross section
dscs = smuthi.scattered_field.scattering_cross_section(
initial_field=plane_wave,
particle_list=par_list,
layer_system=two_layers,
polar_angles=angles)
cext0 = smuthi.scattered_field.extinction_cross_section(
plane_wave, par_list, two_layers)
scat = dscs.integral()
cext = cext0['top'] + cext0['bottom']
return cext, scat
def simsmuthi(wl, parri, par_list, subri=1, topri=1, neff_res=5e-3):
"""
Default smuthi simulation for particles on a substrate
Specular plane wave incidence with user-specified wavelength.
Important note: all particles must be made of the same material!
:param wl: wavelength
:param parri: refractive index data of the particle
:param subri: substrate refractive index (default: 1)
:param topri: refractive index in which the particle is embedded (default: 1)
:return: tuple with extinction and scattering cross-sections
"""
for jj in range(len(par_list)):
par_list[jj].refractive_index = parri
coord.set_default_k_parallel(wl,
neff_resolution=neff_res,
neff_max=subri + 1,
neff_imag=1e-2)
two_layers = smuthi.layers.LayerSystem(thicknesses=[0, 0],
refractive_indices=[topri, subri])
plane_wave = smuthi.initial_field.PlaneWave(
vacuum_wavelength=wl,
polar_angle=0, # from top
azimuthal_angle=0,
polarization=0) # 0=TE 1=TM
if len(par_list) < 3:
simulation = smuthi.simulation.Simulation(layer_system=two_layers,
particle_list=par_list,
initial_field=plane_wave,
solver_type='gmres')
else:
simulation = smuthi.simulation.Simulation(
layer_system=two_layers,
particle_list=par_list,
initial_field=plane_wave,
solver_type='KCSolver',
store_coupling_matrix=False,
coupling_matrix_lookup_resolution=3)
simulation.run()
return simulation
refractive_index=1.52,
radius=100,
l_max=3)
# list of all scattering particles (only one in this case)
one_sphere = [sphere]
# Initial field
plane_wave = smuthi.initial_field.PlaneWave(
vacuum_wavelength=550,
polar_angle=-np.pi, # from top
azimuthal_angle=0,
polarization=0) # 0=TE 1=TM
# Initialize and run simulation
simulation = smuthi.simulation.Simulation(layer_system=two_layers,
particle_list=one_sphere,
initial_field=plane_wave)
simulation.run()
# Show differential scattering cross section
dscs = smuthi.scattered_field.scattering_cross_section(
initial_field=plane_wave,
particle_list=one_sphere,
layer_system=two_layers)
smuthi.graphical_output.show_far_field(dscs,
save_plots=True,
show_plots=False,
outputdir='sphere_on_substrate')
def GetTSCS(WL, core_r, index_NP, samples):
# Initialize a plane wave object the initial field
plane_wave = smuthi.initial_field.PlaneWave(
vacuum_wavelength=WL,
polar_angle=-np.pi, # normal incidence, from top
azimuthal_angle=0,
polarization=1) # 0 stands for TE, 1 stands for TM
# Initialize the layer system object
# The coordinate system is such that the interface between the first two layers defines the plane z=0.
two_layers = smuthi.layers.LayerSystem(
thicknesses=[0, 0], # substrate, ambient
refractive_indices=[1.0, 1.0]) # like aluminum, SiO2, air
# Define the scattering particles
particle_grid = []
spacer = 1.1 * core_r #nm
sphere = smuthi.particles.Sphere(
position=[0, 0, 40], #core_r+spacer],
refractive_index=index_NP,
radius=core_r,
l_max=3) # choose l_max with regard to particle size and material
# higher means more accurate but slower
particle_grid.append(sphere)
# Define contour for Sommerfeld integral
smuthi.coordinates.set_default_k_parallel(
vacuum_wavelength=plane_wave.vacuum_wavelength,
neff_resolution=5e-3, # smaller value means more accurate but slower
neff_max=2) # should be larger than the highest refractive
# index of the layer system
global total_runs
if total_runs == 0:
log_to_terminal = True
print("\n\n\t\tExample of solver output for the first run:\n\n")
total_runs += 1
else:
log_to_terminal = False
# Initialize and run simulation
simulation = smuthi.simulation.Simulation(
layer_system=two_layers,
particle_list=particle_grid,
initial_field=plane_wave,
solver_type='LU',
# solver_type='gmres',
solver_tolerance=1e-5,
store_coupling_matrix=True,
coupling_matrix_lookup_resolution=None,
# store_coupling_matrix=False,
# coupling_matrix_lookup_resolution=5,
coupling_matrix_interpolator_kind='cubic',
log_to_file=False,
log_to_terminal=log_to_terminal)
simulation.run()
p_angles = np.linspace(0, np.pi, samples, dtype=float)
a_angles = np.linspace(0, 2.0 * np.pi, samples, dtype=float)
#print(angles)
scattering_cross_section = smuthi.scattered_field.scattering_cross_section(
initial_field=plane_wave,
particle_list=particle_grid,
layer_system=two_layers,
polar_angles=p_angles,
azimuthal_angles=a_angles)
Q_sca = (scattering_cross_section.top().integral()[0] +
scattering_cross_section.top().integral()[1] +
scattering_cross_section.bottom().integral()[0] +
scattering_cross_section.bottom().integral()[1]).real / (
np.pi * core_r**2)
return Q_sca
def GetTopTSCS(WL, index_chrome, index_gold, l_max, neff_max, sample):
#smuthi.layers.set_precision(1000)
# Initialize the layer system object
# The coordinate system is such that the interface between the
# first two layers defines the plane z=0.
thickness_chrome = sample[1]
thickness_gold = sample[2]
two_layers = smuthi.layers.LayerSystem(
thicknesses=[0, thickness_gold, thickness_chrome,
0], # ambient, substrate
refractive_indices=[1.0, index_gold, index_chrome,
index_glass]) # like glass, air
# Define the scattering particles
particle_grid = []
sphere = smuthi.particles.Sphere(
position=[0, 0, -spacer / 2.0],
refractive_index=index_glass,
radius=spacer / 2.0,
l_max=l_max) # choose l_max with regard to particle size and material
# higher means more accurate but slower
particle_grid.append(sphere)
sphere = smuthi.particles.Sphere(
position=[0, 0, -spacer - core_r * 2 - spacer * 2 - stm_r],
refractive_index=index_gold,
radius=stm_r,
l_max=l_max) # choose l_max with regard to particle size and material
# higher means more accurate but slower
particle_grid.append(sphere)
# Define contour for Sommerfeld integral
alpha = np.linspace(0, 2 * np.pi, 100)
smuthi.coordinates.set_default_k_parallel(
vacuum_wavelength=WL,
neff_resolution=1e-2,
neff_max=neff_max
# ,neff_waypoints=[0,0.9-0.15j, 8.7-0.15j, 8.7, neff_max]
)
# smuthi.coordinates.set_default_k_parallel(vacuum_wavelength=WL,
# neff_resolution=1e-2,
# neff_waypoints=[0,0.9-0.15j, 1.1-0.15j, 1.2, neff_max] )
dipole_source = smuthi.initial_field.DipoleSource(
vacuum_wavelength=WL,
dipole_moment=dipole_moment,
position=[0, 0, -spacer - core_r * 2 - spacer],
# position=[0, 0, -spacer],
azimuthal_angles=alpha)
# Initialize and run simulation
simulation = smuthi.simulation.Simulation(
layer_system=two_layers,
particle_list=particle_grid,
initial_field=dipole_source,
solver_type='LU',
# solver_type='gmres',
solver_tolerance=1e-5,
store_coupling_matrix=True,
coupling_matrix_lookup_resolution=None,
# store_coupling_matrix=False,
# coupling_matrix_lookup_resolution=5,
coupling_matrix_interpolator_kind='cubic',
log_to_file=False,
log_to_terminal=False)
simulation.run()
#polar = np.linspace(0, 0.228857671*np.pi, 100) # 0.21*pi rad == 37.8 grad
polar = np.linspace(0, 0.21 * np.pi, 100) # 0.21*pi rad == 37.8 grad
total_far_field, initial_far_field, scattered_far_field = smuthi.scattered_field.total_far_field(
initial_field=dipole_source,
particle_list=particle_grid,
layer_system=two_layers,
polar_angles=polar)
diss_pow = dipole_source.dissipated_power(particle_grid, two_layers)
assert abs(diss_pow.imag / diss_pow) < 1e-8
diss_pow = diss_pow.real
top_pow, bottom_pow = 0, 0
P0 = dipole_source.dissipated_power_homogeneous_background(
layer_system=two_layers)
top_pow = sum(total_far_field.integral()).real #sum both polarizations
return WL, top_pow, diss_pow, P0, diss_pow / P0
if use_gpu and not cu.use_gpu:
print("Failed to load pycuda, skipping simulation")
sys.exit(1)
print("number of particles = " + str(len(smuthi_spheres)))
simulation = smuthi.simulation.Simulation(
layer_system=two_layers,
particle_list=smuthi_spheres,
initial_field=smuthi_plane_wave,
solver_type='gmres',
store_coupling_matrix=False,
coupling_matrix_interpolator_kind='linear',
coupling_matrix_lookup_resolution=50, #5,
solver_tolerance=1e-4,
length_unit='nm')
prep_time, solution_time, post_time = simulation.run()
log_file = open(projects_directory_location + "/log.txt", 'a')
log_file.write("Prep, Solution, Post times are: " + str(prep_time) +
", " + str(solution_time) + ", " + str(post_time) +
"\n")
log_file.close()
vacuum_wavelength = simulation.initial_field.vacuum_wavelength
dim1vec = np.arange(-1000, 1000 + 25 / 2, 25)
dim2vec = np.arange(-1000, 1000 + 25 / 2, 25)
xarr, yarr = np.meshgrid(dim1vec, dim2vec)
zarr = xarr - xarr - focal_length_nm
scat_fld_exp = sf.scattered_field_piecewise_expansion(
vacuum_wavelength, simulation.particle_list,
def simulate_N_spheres(number_of_spheres=100,
direct_inversion=True,
use_gpu=False,
solver_tolerance=5e-4,
lookup_resolution=5,
interpolation_order='linear',
make_illustrations=False):
# Initialize the layer system: substrate (glass) and ambient (air)
two_layers = smuthi.layers.LayerSystem(thicknesses=[0, 0],
refractive_indices=[1.52, 1])
# Initial field
plane_wave = smuthi.initial_field.PlaneWave(
vacuum_wavelength=550,
polar_angle=np.pi, # from top
azimuthal_angle=0,
polarization=0) # 0=TE 1=TM
spheres_list = vogel_spiral(number_of_spheres)
# Initialize and run simulation
cu.enable_gpu(use_gpu)
if use_gpu and not cu.use_gpu:
print("Failed to load pycuda, skipping simulation")
return [0, 0, 0]
if direct_inversion:
simulation = smuthi.simulation.Simulation(layer_system=two_layers,
particle_list=spheres_list,
initial_field=plane_wave)
else:
simulation = smuthi.simulation.Simulation(
layer_system=two_layers,
particle_list=spheres_list,
initial_field=plane_wave,
solver_type='gmres',
solver_tolerance=solver_tolerance,
store_coupling_matrix=False,
coupling_matrix_lookup_resolution=lookup_resolution,
coupling_matrix_interpolator_kind=interpolation_order)
preparation_time, solution_time, _ = simulation.run()
# compute cross section
ecs = smuthi.postprocessing.far_field.extinction_cross_section(
initial_field=plane_wave,
particle_list=spheres_list,
layer_system=two_layers)
if make_illustrations:
azimuthal_angles = np.arange(0, 361, 0.5, dtype=float) * np.pi / 180
polar_angles = np.arange(0, 181, 0.25, dtype=float) * np.pi / 180
dscs = smuthi.postprocessing.far_field.scattering_cross_section(
initial_field=plane_wave,
particle_list=spheres_list,
layer_system=two_layers,
polar_angles=polar_angles,
azimuthal_angles=azimuthal_angles,
)
# display differential scattering cross section
smuthi.postprocessing.graphical_output.show_far_field(
far_field=dscs,
save_plots=True,
show_plots=True,
save_data=False,
tag='dscs_%ispheres' % number_of_spheres,
log_scale=True)
xlim = max([abs(sphere.position[0]) for sphere in spheres_list]) * 1.1
plt.figure()
plt.xlim([-xlim, xlim])
plt.xlabel('x (nm)')
plt.ylabel('y (nm)')
plt.ylim([-xlim, xlim])
plt.gca().set_aspect("equal")
plt.title("Vogel spiral with %i spheres" % number_of_spheres)
smuthi.postprocessing.graphical_output.plot_particles(
-1e5, 1e5, -1e5, 1e5, 0, 0, spheres_list, 1000, False)
plt.savefig("vogel_spiral_%i.png" % number_of_spheres)
return [(ecs["top"] + ecs["bottom"]).real, preparation_time, solution_time]