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.initial_field as init
import smuthi.particles as part
import smuthi.coordinates as coord
import smuthi.simulation as simul
import smuthi.layers as lay
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],
reference_point=beam_focal_point,
beam_waist=beam_waist,
k_parallel_array=beam_neff_array *
coord.angular_frequency(vacuum_wavelength))
# initialize simulation object
simulation_direct = simul.Simulation(layer_system=lay_sys,
particle_list=particle_list,
initial_field=init_fld,
solver_type='LU',
store_coupling_matrix=True,
log_to_terminal=False)
simulation_direct.run()
coefficients_direct = particle_list[0].scattered_field.coefficients
cu.enable_gpu()
simulation_lookup_linear_gpu = simul.Simulation(
layer_system=lay_sys,
particle_list=particle_list,
initial_field=init_fld,
solver_type='gmres',
store_coupling_matrix=False,
coupling_matrix_lookup_resolution=lookup_resol,
coupling_matrix_interpolator_kind='linear',
log_to_terminal=False)
simulation_lookup_linear_gpu.run()
coefficients_lookup_linear_gpu = particle_list[0].scattered_field.coefficients
simulation_lookup_cubic_gpu = simul.Simulation(
layer_system=lay_sys,
particle_list=particle_list,