def run(self):
"""Start the simulation."""
self.print_simulation_header()
# check if default contour exists, otherwise set a contour
if coord.default_k_parallel is None:
neff_resolution = 5e-3
neff_max = max(
np.array(self.layer_system.refractive_indices).real) + 1
neff_imag = 5e-2
coord.set_default_k_parallel(
vacuum_wavelength=self.initial_field.vacuum_wavelength,
neff_resolution=neff_resolution,
neff_max=neff_max,
neff_imag=neff_imag)
self.initialize_linear_system()
self.linear_system.prepare()
self.linear_system.solve()
# post processing
if self.post_processing:
self.post_processing.run(self)
if self.save_after_run:
self.save(self.output_dir + '/simulation.p')
sys.stdout.write('\n')
sys.stdout.flush()
plt.show()
def test_w_against_wr():
coord.set_default_k_parallel(wl, [0, 0.8, 0.8 - 0.1j, 2.1 - 0.1j, 2.1, 7],
2e-3)
laysys_air_1 = lay.LayerSystem(thicknesses=[0, 0],
refractive_indices=[1, 1])
laysys_air_2 = lay.LayerSystem(thicknesses=[0, 250, 0],
refractive_indices=[1, 1, 1])
part1 = part.Sphere(position=[100, -100, 200],
refractive_index=1.7,
radius=100,
l_max=2,
m_max=2)
part2 = part.Sphere(position=[-100, 200, 400],
refractive_index=1.7,
radius=100,
l_max=2,
m_max=2)
w_air_1 = coup.direct_coupling_block(wl, part1, part2, laysys_air_1)
wr_air_2 = coup.layer_mediated_coupling_block(wl, part1, part2,
laysys_air_2)
error = wr_air_2 - w_air_1
np.testing.assert_almost_equal(wr_air_2, w_air_1, decimal=4)
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
# Parameter input ----------------------------
ld = 550
rD = [300, -200, 100]
D = [1e7, 2e7, 3e7]
thick = [0, 200, 200, 0]
n = [1, 1.5, 2 + 1e-2j, 1 + 5j]
waypoints = [0, 0.8, 0.8 - 0.1j, 2.1 - 0.1j, 2.1, 4]
neff_discr = 1e-2
rS = [100, 200, 300]
nS = 1.5
RS = 100
# --------------------------------------------
coord.set_default_k_parallel(vacuum_wavelength=ld,
neff_waypoints=waypoints,
neff_resolution=neff_discr)
dipole = init.DipoleSource(vacuum_wavelength=ld, dipole_moment=D, position=rD)
laysys = lay.LayerSystem(thicknesses=thick, refractive_indices=n)
particle = smuthi.particles.Sphere(position=rS,
l_max=3,
m_max=3,
refractive_index=nS,
radius=RS)
simulation = simul.Simulation(layer_system=laysys,
particle_list=[particle],
initial_field=dipole)
aI = dipole.spherical_wave_expansion(particle, laysys)
substrate_refractive_index = 1.52
sphere_refractive_index = 2.4
distance_sphere_substrate = 50
plane_wave_polar_angle = np.pi
plane_wave_azimuthal_angle = 0
plane_wave_polarization = 0
plane_wave_amplitude = 1
lmax = 3
neff_waypoints = [0, 0.5, 0.8 - 0.1j, 2 - 0.1j, 2.5, 4]
neff_discr = 1e-3
farfield_neff_waypoints = [0, 1]
farfield_neff_discr = 1e-2
# --------------------------------------------
coord.set_default_k_parallel(vacuum_wavelength, neff_waypoints, neff_discr)
# initialize particle object
part1 = part.Sphere(position=[0, 0, distance_sphere_substrate + sphere_radius],
refractive_index=sphere_refractive_index,
radius=sphere_radius,
l_max=lmax,
m_max=lmax)
particle_list = [part1]
# initialize layer system object
lay_sys = lay.LayerSystem(
[0, 0], [substrate_refractive_index, surrounding_medium_refractive_index])
# initialize initial field object
init_fld = init.PlaneWave(vacuum_wavelength=vacuum_wavelength,
wl = np.array([370])
wl = np.linspace(250, 500,
21) # another example declaration of wavelengths
subri = 2 # substrate refractive index
# nkdata = ms.LoadNkData(wl, fname) # use if you want to import Si data from Schinke
nkdata = 0 * wl + 4 # particle refractive index
CC = 7000
pos = np.array([[0, 0, -rad], [CC * rad, CC * rad,
-rad]]) # list of particle positions
# pos = ms.LoadPosFile(posname, CC, rad, -rad) # loads position from posname and scales it to match rad
N_particles = pos.shape[0]
cext_tot = []
for ii in range(len(wl)):
# set_default_k_parallel is extremely tricky function from Amos. Use with care.
coord.set_default_k_parallel(wl[ii],
neff_resolution=5e-3,
neff_max=subri + 1)
two_layers = layers.LayerSystem(thicknesses=[0, 0],
refractive_indices=[1, subri])
par_list = ms.PrepareIdenticalParticles(positions=pos,
radius=rad,
l_max=1,
ref_ind=nkdata[ii])
k0 = 2 * np.pi / wl[ii]
c = -6 * 1j * k0**(-3) / 4
M = conversionmatrix(N_particles, c) # not too smart!
Sr = layercoupling(wl[ii], par_list, two_layers, M)
S = particlecoupling(wl[ii], pos)
alfinv = inversepolarizabilities(par_list, wl[ii])
Einc = initial_field(wl[ii], par_list, two_layers)
p = solve(alfinv, S, Sr, Einc)
import smuthi.scattered_field as sf
import smuthi.graphical_output as go
import smuthi.cuda_sources as cu
import numpy as np
import scipy.interpolate as interp
import matplotlib.pyplot as plt
import os
# Enable GPU usage. Uncomment if you receive GPU related errors
cu.enable_gpu()
vacuum_wavelength = 550
# Sommerfeld integral contour
coord.set_default_k_parallel(vacuum_wavelength,
neff_resolution=1e-2,
neff_max=3)
# Set the multipole truncation order
# We invite the user to play with this parameter to see how it affects
# accuracy and runtime.
lmax = 5
# particles
sphere = part.Sphere(position=[300, 300, 250],
refractive_index=3,
radius=120,
l_max=lmax)
cylinder = part.FiniteCylinder(position=[300, -300, 250],
refractive_index=3,
def read_input_yaml(filename):
"""Parse input file
Args:
filename (str): relative path and filename of input file
Returns:
smuthi.simulation.Simulation object containing the params of the input file
"""
print('Reading ' + os.path.abspath(filename))
with open(filename, 'r') as input_file:
input_data = yaml.load(input_file.read())
cu.enable_gpu(input_data.get('enable GPU', False))
# wavelength
wl = float(input_data['vacuum wavelength'])
# set default coordinate arrays
angle_unit = input_data.get('angle unit')
if angle_unit == 'degree':
angle_factor = np.pi / 180
else:
angle_factor = 1
angle_resolution = input_data.get(
'angular resolution', np.pi / 180 / angle_factor) * angle_factor
coord.default_azimuthal_angles = np.arange(
0, 2 * np.pi + angle_resolution / 2, angle_resolution)
coord.default_polar_angles = np.arange(0, np.pi + angle_resolution / 2,
angle_resolution)
neff_resolution = float(input_data.get('n_effective resolution', 1e-2))
neff_max = input_data.get('max n_effective')
if neff_max is None:
ref_ind = [
float(n) for n in input_data['layer system']['refractive indices']
]
neff_max = max(np.array(ref_ind).real) + 1
neff_imag = float(input_data.get('n_effective imaginary deflection', 5e-2))
coord.set_default_k_parallel(vacuum_wavelength=wl,
neff_resolution=neff_resolution,
neff_max=neff_max,
neff_imag=neff_imag)
# initialize simulation
lookup_resolution = input_data.get('coupling matrix lookup resolution',
None)
if lookup_resolution is not None and lookup_resolution <= 0:
lookup_resolution = None
simulation = smuthi.simulation.Simulation(
solver_type=input_data.get('solver type', 'LU'),
solver_tolerance=float(input_data.get('solver tolerance', 1e-4)),
store_coupling_matrix=input_data.get('store coupling matrix', True),
coupling_matrix_lookup_resolution=lookup_resolution,
coupling_matrix_interpolator_kind=input_data.get(
'interpolation order', 'linear'),
input_file=filename,
length_unit=input_data.get('length unit'),
output_dir=input_data.get('output folder'),
save_after_run=input_data.get('save simulation'))
# particle collection
particle_list = []
particle_input = input_data['scattering particles']
if isinstance(particle_input, str):
particle_type = 'sphere'
with open(particle_input, 'r') as particle_specs_file:
for line in particle_specs_file:
if len(line.split()) > 0:
if line.split()[-1] == 'spheres':
particle_type = 'sphere'
elif line.split()[-1] == 'spheroids':
particle_type = 'spheroid'
elif line.split()[-1] == 'cylinders':
particle_type = 'finite cylinder'
if not line.split()[0] == '#':
numeric_line_data = [float(x) for x in line.split()]
pos = numeric_line_data[:3]
if particle_type == 'sphere':
r = numeric_line_data[3]
n = numeric_line_data[4] + 1j * numeric_line_data[5]
l_max = int(numeric_line_data[6])
m_max = int(numeric_line_data[7])
particle_list.append(
part.Sphere(position=pos,
refractive_index=n,
radius=r,
l_max=l_max,
m_max=m_max))
if particle_type == 'spheroid':
c = numeric_line_data[3]
a = numeric_line_data[4]
beta = numeric_line_data[5]
alpha = numeric_line_data[6]
n = numeric_line_data[7] + 1j * numeric_line_data[8]
l_max = int(numeric_line_data[9])
m_max = int(numeric_line_data[10])
particle_list.append(
part.Spheroid(position=pos,
polar_angle=beta,
azimuthal_angle=beta,
refractive_index=n,
semi_axis_c=c,
semi_axis_a=a,
l_max=l_max,
m_max=m_max))
if particle_type == 'finite cylinder':
r = numeric_line_data[3]
h = numeric_line_data[4]
beta = numeric_line_data[5]
alpha = numeric_line_data[6]
n = numeric_line_data[7] + 1j * numeric_line_data[8]
l_max = int(numeric_line_data[9])
m_max = int(numeric_line_data[10])
particle_list.append(
part.FiniteCylinder(position=pos,
polar_angle=beta,
azimuthal_angle=beta,
refractive_index=n,
cylinder_radius=r,
cylinder_height=h,
l_max=l_max,
m_max=m_max))
else:
for prtcl in input_data['scattering particles']:
n = (float(prtcl['refractive index']) +
1j * float(prtcl['extinction coefficient']))
pos = [
float(prtcl['position'][0]),
float(prtcl['position'][1]),
float(prtcl['position'][2])
]
l_max = int(prtcl['l_max'])
m_max = int(prtcl.get('m_max', l_max))
if prtcl['shape'] == 'sphere':
r = float(prtcl['radius'])
particle_list.append(
part.Sphere(position=pos,
refractive_index=n,
radius=r,
l_max=l_max,
m_max=m_max))
else:
nfmds_settings = prtcl.get('NFM-DS settings', {})
use_ds = nfmds_settings.get('use discrete sources', True)
nint = nfmds_settings.get('nint', 200)
nrank = nfmds_settings.get('nrank', l_max + 2)
t_matrix_method = {
'use discrete sources': use_ds,
'nint': nint,
'nrank': nrank
}
polar_angle = prtcl.get('polar angle', 0)
azimuthal_angle = prtcl.get('azimuthal angle', 0)
if prtcl['shape'] == 'spheroid':
c = float(prtcl['semi axis c'])
a = float(prtcl['semi axis a'])
particle_list.append(
part.Spheroid(position=pos,
polar_angle=polar_angle,
azimuthal_angle=azimuthal_angle,
refractive_index=n,
semi_axis_a=a,
semi_axis_c=c,
l_max=l_max,
m_max=m_max,
t_matrix_method=t_matrix_method))
elif prtcl['shape'] == 'finite cylinder':
h = float(prtcl['cylinder height'])
r = float(prtcl['cylinder radius'])
particle_list.append(
part.FiniteCylinder(position=pos,
polar_angle=polar_angle,
azimuthal_angle=azimuthal_angle,
refractive_index=n,
cylinder_radius=r,
cylinder_height=h,
l_max=l_max,
m_max=m_max,
t_matrix_method=t_matrix_method))
else:
raise ValueError(
'Currently, only spheres, spheroids and finite cylinders are implemented'
)
simulation.particle_list = particle_list
# layer system
thick = [float(d) for d in input_data['layer system']['thicknesses']]
ref_ind = [
float(n) for n in input_data['layer system']['refractive indices']
]
ext_coeff = [
float(n) for n in input_data['layer system']['extinction coefficients']
]
ref_ind = np.array(ref_ind) + 1j * np.array(ext_coeff)
ref_ind = ref_ind.tolist()
simulation.layer_system = lay.LayerSystem(thicknesses=thick,
refractive_indices=ref_ind)
# initial field
infld = input_data['initial field']
if infld['type'] == 'plane wave':
a = float(infld.get('amplitude', 1))
pol_ang = angle_factor * float(infld['polar angle'])
az_ang = angle_factor * float(infld['azimuthal angle'])
if infld['polarization'] == 'TE':
pol = 0
elif infld['polarization'] == 'TM':
pol = 1
else:
raise ValueError('polarization must be "TE" or "TM"')
ref = [
float(infld.get('reference point', [0, 0, 0])[0]),
float(infld.get('reference point', [0, 0, 0])[1]),
float(infld.get('reference point', [0, 0, 0])[2])
]
initial_field = init.PlaneWave(vacuum_wavelength=wl,
polar_angle=pol_ang,
azimuthal_angle=az_ang,
polarization=pol,
amplitude=a,
reference_point=ref)
elif infld['type'] == 'Gaussian beam':
a = float(infld['amplitude'])
pol_ang = angle_factor * float(infld['polar angle'])
az_ang = angle_factor * float(infld['azimuthal angle'])
if infld['polarization'] == 'TE':
pol = 0
elif infld['polarization'] == 'TM':
pol = 1
else:
raise ValueError('polarization must be "TE" or "TM"')
ref = [
float(infld['focus point'][0]),
float(infld['focus point'][1]),
float(infld['focus point'][2])
]
ang_res = infld.get('angular resolution',
np.pi / 180 / ang_fac) * ang_fac
bet_arr = np.arange(0, np.pi / 2, ang_res)
if pol_ang <= np.pi:
kparr = np.sin(bet_arr) * simulation.layer_system.wavenumber(
layer_number=0, vacuum_wavelength=wl)
else:
kparr = np.sin(bet_arr) * simulation.layer_system.wavenumber(
layer_number=-1, vacuum_wavelength=wl)
wst = infld['beam waist']
aarr = np.concatenate([np.arange(0, 2 * np.pi, ang_res), [2 * np.pi]])
initial_field = init.GaussianBeam(vacuum_wavelength=wl,
polar_angle=pol_ang,
azimuthal_angle=az_ang,
polarization=pol,
beam_waist=wst,
k_parallel_array=kparr,
azimuthal_angles_array=aarr,
amplitude=a,
reference_point=ref)
elif infld['type'] == 'dipole source':
pos = [float(infld['position'][i]) for i in range(3)]
mom = [float(infld['dipole moment'][i]) for i in range(3)]
initial_field = init.DipoleSource(vacuum_wavelength=wl,
dipole_moment=mom,
position=pos)
elif infld['type'] == 'dipole collection':
initial_field = init.DipoleCollection(vacuum_wavelength=wl)
dipoles = infld['dipoles']
for dipole in dipoles:
pos = [float(dipole['position'][i]) for i in range(3)]
mom = [float(dipole['dipole moment'][i]) for i in range(3)]
dip = init.DipoleSource(vacuum_wavelength=wl,
dipole_moment=mom,
position=pos)
initial_field.append(dip)
simulation.initial_field = initial_field
# post processing
simulation.post_processing = pp.PostProcessing()
if input_data.get('post processing'):
for item in input_data['post processing']:
if item['task'] == 'evaluate far field':
simulation.post_processing.tasks.append(item)
elif item['task'] == 'evaluate near field':
simulation.post_processing.tasks.append(item)
return simulation
import smuthi.scattered_field as sf
import numpy as np
from smuthi.coordinates import default_azimuthal_angles
ld = 550
rD1 = [100, -100, 100]
D1 = [1e7, 2e7, 3e7]
rD2 = [-100, 100, -100]
D2 = [-2e7, 3e7, 1e7]
# waypoints = [0, 0.8, 0.8-0.1j, 2.1-0.1j, 2.1, 3]
neff_max = 3
neff_discr = 5e-3
coord.set_default_k_parallel(vacuum_wavelength=ld,
neff_resolution=neff_discr,
neff_max=neff_max)
#coord.default_k_parallel = np.array([0, 0.5*2*np.pi/ld])
# initialize particle object
# first two spheres in top layer
sphere1 = part.Sphere(position=[200, 200, 500],
refractive_index=2.4 + 0.0j,
radius=110,
l_max=3,
m_max=3)
sphere2 = part.Sphere(position=[200, -200, 500],
refractive_index=2.4 + 0.0j,
radius=110,
l_max=3,
m_max=3)
#idx.set_swe_specs(l_max=2)
wl = 550
part1 = part.Sphere(position=[100, -100, 200],
refractive_index=1.7,
radius=100,
l_max=2,
m_max=2)
part2 = part.Sphere(position=[-100, 200, 300],
refractive_index=1.7,
radius=100,
l_max=2,
m_max=2)
coord.set_default_k_parallel(wl, [0, 0.8, 0.8 - 0.1j, 2.1 - 0.1j, 2.1, 3],
2e-3)
def test_wr_against_prototype():
laysys_substrate = lay.LayerSystem(thicknesses=[0, 0],
refractive_indices=[2 + 0.1j, 1])
wr_sub00 = coup.layer_mediated_coupling_block(wl, part1, part1,
laysys_substrate)
wr_sub01 = coup.layer_mediated_coupling_block(wl, part1, part2,
laysys_substrate)
wr_sub_0000 = -0.116909038698419 - 0.013001770175717j
assert abs((wr_sub00[0, 0] - wr_sub_0000) / wr_sub_0000) < 1e-5
wr_sub_0010 = 0.051728301055665 - 0.030410521218822j
assert abs((wr_sub01[0, 0] - wr_sub_0010) / wr_sub_0010) < 1e-5
