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