def sim(separation):
"""perform scattering simulation"""
L = separation + 2*radius + 2*pml_monitor_gap + 2*particle_monitor_gap + 2*pml.thickness
cell = meep.Vector3(L,L,L)
p1 = meep.Vector3(-separation/2, 0, 0)
p2 = meep.Vector3(separation/2, 0, 0)
geometry = [meep.Sphere(center=p1,
radius=radius,
material=gold),
meep.Sphere(center=p2,
radius=radius,
material=gold)]
scat = meep.Simulation(cell_size=cell,
boundary_layers=[pml],
geometry=geometry,
resolution=resolution)
scat.init_fields()
source(scat)
L = 2*radius + 2*particle_monitor_gap
Fx = meep_ext.add_force_box(scat, fcen, 0, 1, p2, [L,L,L], meep.X)
Fy = meep_ext.add_force_box(scat, fcen, 0, 1, p2, [L,L,L], meep.Y)
Fz = meep_ext.add_force_box(scat, fcen, 0, 1, p2, [L,L,L], meep.Z)
# scat.run(until_after_sources=8*um)
scat.run(until_after_sources=meep.stop_when_fields_decayed(.5*um, meep.Ex,
pt=p2-meep.Vector3(0,0,L/2), decay_by=1e-5))
return {'Fx': np.array(meep.get_forces(Fx))[0], 'Fy': np.array(meep.get_forces(Fy))[0], 'Fz': np.array(meep.get_forces(Fz))[0]}
def sim(separation, monitor_size, unique_id):
"""perform scattering simulation"""
monitor_size = np.asarray(monitor_size)
cell_size = monitor_size + 2*pml_monitor_gap + 2*pml.thickness
cell = meep.Vector3(*cell_size)
p1 = meep.Vector3(-separation/2, 0, 0)
p2 = meep.Vector3(separation/2, 0, 0)
geometry = [meep.Sphere(center=p1,
radius=radius,
material=gold),
meep.Sphere(center=p2,
radius=radius,
material=gold)]
scat = meep.Simulation(cell_size=cell,
boundary_layers=[pml],
geometry=geometry,
default_material=medium,
resolution=resolution)
scat.init_fields()
source(scat)
flux_box_absorb = meep_ext.add_flux_box(scat, fcen, 0, 1, [0,0,0], monitor_size)
flux_box_scat = meep_ext.add_flux_box(scat, fcen, 0, 1, [0,0,0], monitor_size)
scat.load_minus_flux(norm_file_ext.format(unique_id), flux_box_scat)
# scat.run(until_after_sources=8*um)
scat.run(until_after_sources=meep.stop_when_fields_decayed(.5*um, polarization,
pt=p2 - meep.Vector3(0,0,monitor_size[2]/2), decay_by=1e-4))
return {'scattering': np.array(meep.get_fluxes(flux_box_scat)), 'absorption': -np.array(meep.get_fluxes(flux_box_absorb))}
def test_epsilon_warning(self):
## fields blow up using dispersive material
## when compiled using single precision
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter("always")
from meep.materials import Si
self.assertEqual(len(w), 0)
from meep.materials import Mo
geom = [mp.Sphere(radius=0.2, material=Mo)]
sim = self.init_simple_simulation(geometry=geom)
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter("always")
sim.run(until=5)
self.assertGreater(len(w), 0)
self.assertIn("Epsilon", str(w[0].message))
from meep.materials import SiO2
geom = [mp.Sphere(radius=0.2, material=SiO2)]
sim = self.init_simple_simulation(geometry=geom)
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter("always")
sim.run(until=5)
self.assertEqual(len(w), 1)
self.assertNotIn("Epsilon", str(w[0].message))
def test_check_material_frequencies(self):
mat = mp.Medium(valid_freq_range=mp.FreqRange(min=10, max=20))
invalid_sources = [
[mp.Source(mp.GaussianSource(5, fwidth=1), mp.Ez, mp.Vector3())],
[mp.Source(mp.ContinuousSource(10, fwidth=1), mp.Ez, mp.Vector3())],
[mp.Source(mp.GaussianSource(10, width=1), mp.Ez, mp.Vector3())],
[mp.Source(mp.GaussianSource(20, width=1), mp.Ez, mp.Vector3())],
]
cell_size = mp.Vector3(5, 5)
resolution = 5
def check_warnings(sim, should_warn=True):
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter("always")
sim.run(until=5)
if should_warn:
self.assertEqual(len(w), 1)
self.assertIn("material", str(w[-1].message))
else:
self.assertEqual(len(w), 0)
geom = [mp.Sphere(0.2, material=mat)]
for s in invalid_sources:
# Check for invalid extra_materials
sim = mp.Simulation(cell_size=cell_size, resolution=resolution, sources=s, extra_materials=[mat])
check_warnings(sim)
# Check for invalid geometry materials
sim = mp.Simulation(cell_size=cell_size, resolution=resolution, sources=s, geometry=geom)
check_warnings(sim)
valid_sources = [
[mp.Source(mp.GaussianSource(15, fwidth=1), mp.Ez, mp.Vector3())],
[mp.Source(mp.ContinuousSource(15, width=5), mp.Ez, mp.Vector3())]
]
for s in valid_sources:
sim = mp.Simulation(cell_size=cell_size, resolution=resolution, sources=s, extra_materials=[mat])
check_warnings(sim, False)
# Check DFT frequencies
# Invalid extra_materials
sim = mp.Simulation(cell_size=cell_size, resolution=resolution, sources=valid_sources[0],
extra_materials=[mat])
fregion = mp.FluxRegion(center=mp.Vector3(0, 1), size=mp.Vector3(2, 2), direction=mp.X)
sim.add_flux(18, 6, 2, fregion)
check_warnings(sim)
# Invalid geometry material
sim = mp.Simulation(cell_size=cell_size, resolution=resolution, sources=valid_sources[0], geometry=geom)
sim.add_flux(18, 6, 2, fregion)
check_warnings(sim)
def __init__(self, dir_name, wavelength, cyt_absorb):
self.base_directory = base_directory + str(dir_name)
self.wavelength = wavelength
self.cyt_absorb = cyt_absorb
self.frequency = 1 / wavelength
# Calculate wavelengths dependent on RI
self.wavelength_in_media = wavelength / ri_media
self.wavelength_in_cytoplasm = wavelength / ri_cytoplasm
max_freq = self.frequency - 0.01
min_freq = self.frequency + 0.01
self.pulse_width = abs(max_freq - min_freq)
cell = mp.Vector3(sxx, sxy, 0)
pml_layers = [mp.PML(dpml)]
cytoplasm_material = mp.Medium(index=ri_cytoplasm,
D_conductivity=2 * math.pi * self.frequency * (cyt_absorb / (ri_cytoplasm ** 2)))
cytoplasm_region = mp.Sphere(radius=cell_radius,
center=mp.Vector3(0, 0),
material=cytoplasm_material)
geometry = [cytoplasm_region]
# Sources
kdir = mp.Vector3(1, 0, 0) # direction of k (length is irrelevant)
n = ri_media # refractive index of material containing the source
k = kdir.unit().scale(2 * math.pi * self.frequency * n) # k with correct length
def pw_amp(k, x0):
def _pw_amp(x):
return cmath.exp(1j * k.dot(x + x0))
return _pw_amp
source = [
mp.Source(
mp.ContinuousSource(frequency=self.frequency, fwidth=self.pulse_width), # along x axis
component=mp.Ez,
center=mp.Vector3(-0.5 * simulation_size, 0), # x, ,y ,z
size=mp.Vector3(0, sxy, 0),
amp_func=pw_amp(k, mp.Vector3(x=-0.5 * simulation_size))
)
]
sim = mp.Simulation(
cell_size=cell,
sources=source,
boundary_layers=pml_layers,
resolution=resolution,
geometry=geometry,
default_material=mp.Medium(index=ri_media),
force_complex_fields=complex_f,
eps_averaging=eps_av,
)
sim.use_output_directory(self.base_directory)
sim.run(mp.at_every(0.6, mp.output_png(mp.Ez, "-Zc/data/home/bt16268/simInput/customColour.txt")), until=t)
def sweep_dis(l, sources, dis_mat, tstop, span, pos, frq):
if sources == "x":
sources_use = sourcesx
if sources == "z":
sources_use = sourcesz
geometryAu = [
mp.Sphere(material=Au, center=mp.Vector3(x=r + dis_mat[l]), radius=r)
]
frqs, p_flux = purcell_cal(sources_use, geometryAu, tstop, span, pos, frq)
return p_flux
def main(args):
sx = 4.0 #spatial extent along x including pmls (μm)
sy = 4.0
sz = 4.0
dpml = 1.0
cell = mp.Vector3(sx, sy, sz)
pml_layers = [mp.PML(dpml)]
geometry = [
mp.Sphere(radius=0.7, center=mp.Vector3(0, 0, 0), material=Graph),
mp.Sphere(radius=0.5,
center=mp.Vector3(0, 0, 0),
material=mp.Medium(epsilon=12.25))
]
resolution = args.res
wvl = args.wvl / 1000 #convert args.wvl from nm to μm
fcen = 1 / wvl
df = 0.1 * fcen
nfreq = 1
print("wavelength =", wvl, "μm")
print("center frequency =", fcen, "1/μm")
source = [
mp.Source(mp.GaussianSource(fcen, df, nfreq),
component=mp.Ex,
center=mp.Vector3(0, 0.705, 0))
]
symmetries = [mp.Mirror(mp.X), mp.Mirror(mp.Z)]
sim = mp.Simulation(cell_size=cell,
geometry=geometry,
sources=source,
resolution=resolution,
boundary_layers=pml_layers)
pt = mp.Vector3(0, 0.75, 0)
sim.run(mp.dft_ldos(fcen, df, nfreq),
until_after_sources=mp.stop_when_fields_decayed(
20, mp.Ex, pt, 1e-9))
def __init__(self, dir_name, wavelength, cyt_absorb):
self.base_directory = base_directory + str(dir_name)
self.wavelength = wavelength
self.cyt_absorb = cyt_absorb
self.frequency = 1 / wavelength
# Calculate wavelengths dependent on RI
self.wavelength_in_media = wavelength / ri_media
self.wavelength_in_cytoplasm = wavelength / ri_cytoplasm
max_freq = self.frequency - 0.01
min_freq = self.frequency + 0.01
self.pulse_width = abs(max_freq - min_freq)
cell = mp.Vector3(sxx, sxy, 0)
pml_layers = [mp.PML(dpml)]
cytoplasm_material = mp.Medium(index=ri_cytoplasm,
D_conductivity=2 * math.pi *
self.frequency * (cyt_absorb /
(ri_cytoplasm**2)))
cytoplasm_region = mp.Sphere(radius=cell_radius,
center=mp.Vector3(0, 0),
material=cytoplasm_material)
geometry = []
source = [
mp.Source(mp.ContinuousSource(frequency=self.frequency,
fwidth=self.pulse_width),
compone=mp.Ez,
center=(mp.Vector3(-0.5 * simulation_size, 0)),
size=mp.Vector3(0, 10))
]
sim = mp.Simulation(
cell_size=cell,
sources=source,
boundary_layers=pml_layers,
resolution=resolution,
geometry=geometry,
default_material=mp.Medium(index=ri_media),
force_complex_fields=complex_f,
eps_averaging=eps_av,
)
sim.use_output_directory(self.base_directory)
sim.run(mp.at_every(
0.6,
mp.output_png(mp.Ez,
"-Zc/data/home/bt16268/simInput/customColour.txt")),
until=t)
def test_epsilon_warning(self):
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter("always")
from materials_library import Si
self.assertEqual(len(w), 0)
from materials_library import Mo
geom = [mp.Sphere(radius=0.2, material=Mo)]
sim = self.init_simple_simulation(geometry=geom)
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter("always")
sim.run(until=5)
self.assertGreater(len(w), 0)
self.assertIn("Epsilon", str(w[0].message))
from materials_library import SiO2
geom = [mp.Sphere(radius=0.2, material=SiO2)]
sim = self.init_simple_simulation(geometry=geom)
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter("always")
sim.run(until=5)
self.assertEqual(len(w), 1)
self.assertNotIn("Epsilon", str(w[0].message))
def test_geometric_object_duplicates_xyz(self):
rad = 1
s = mp.Sphere(rad)
res = mp.geometric_object_duplicates(mp.Vector3(1, 1, 1), 1, 5, s)
expected = [
mp.Sphere(rad, center=mp.Vector3(1, 1, 1)),
mp.Sphere(rad, center=mp.Vector3(2, 2, 2)),
mp.Sphere(rad, center=mp.Vector3(3, 3, 3)),
mp.Sphere(rad, center=mp.Vector3(4, 4, 4)),
mp.Sphere(rad, center=mp.Vector3(5, 5, 5))
]
for r, e in zip(res, expected):
self.assertEqual(r.center, e.center)
def test_geometric_object_duplicates_x(self):
rad = 1
s = mp.Sphere(rad)
res = mp.geometric_object_duplicates(mp.Vector3(x=1), 1, 5, s)
expected = [
mp.Sphere(rad, center=mp.Vector3(x=1)),
mp.Sphere(rad, center=mp.Vector3(x=2)),
mp.Sphere(rad, center=mp.Vector3(x=3)),
mp.Sphere(rad, center=mp.Vector3(x=4)),
mp.Sphere(rad, center=mp.Vector3(x=5))
]
for r, e in zip(res, expected):
self.assertEqual(r.center, e.center)
def geo2D_spherical_pc(n_matrix,
n_substrate,
film_xsize,
substrate_xsize,
film_ysize,
n_layers,
film_base_x,
sph_radius,
sph_spacing,
layer_offset,
sph_x_offset=0):
"""
Generate a layered structure with spheres. Within a layer the spheres are hexagonally packed
"""
matrix_block = mp.Block(size=mp.Vector3(film_xsize, film_ysize, 1e20),
center=mp.Vector3(film_base_x - film_xsize / 2),
material=mp.Medium(epsilon=n_matrix**2))
si_block = mp.Block(size=mp.Vector3(substrate_xsize, film_ysize, 1e20),
center=mp.Vector3(film_base_x + substrate_xsize / 2, 0,
0),
material=mp.Medium(epsilon=n_substrate**2))
print(n_substrate)
spheres = [si_block, matrix_block]
#spheres = []
for n in range(n_layers):
x = film_base_x - film_xsize * (n + 0.5) / n_layers + sph_x_offset
offset = layer_offset[n]
num_spheres = int(film_ysize / sph_spacing)
sphere_layer = [
mp.Sphere(radius=sph_radius,
center=mp.Vector3(x, y + offset - film_ysize / 2, 0),
material=mp.Medium(epsilon=1))
for y in np.linspace(0, film_ysize, num_spheres)
]
spheres = spheres + sphere_layer
return spheres
import meep as mp
import numpy as np
import math
cell_size = mp.Vector3(2, 2, 2)
geometry = [ #mp.Block(center=mp.Vector3(0,0,0), size=cell_size, material=mp.air),
mp.Sphere(center=mp.Vector3(0, 0, 0), radius=1, material=mp.metal)
]
sim = mp.Simulation(resolution=50, cell_size=cell_size, geometry=geometry)
sim.init_sim()
eps_data = sim.get_epsilon()
#eps_data = sim.get_array()
#sim.plot3D(eps_data)
#from mayavi import mlab
#s = mlab.contour3d()
#mlab.show()
#mlab.savefig(filename='test2.png')
from mayavi import mlab
s = mlab.contour3d(eps_data, colormap="hsv")
#mlab.show()
mlab.savefig('Sphere3D.pdf')
def compute_resonant_mode_3d(use_matgrid=True):
resolution = 25
wvl = 1.27
fcen = 1 / wvl
df = 0.02 * fcen
nSi = 3.45
Si = mp.Medium(index=nSi)
nSiO2 = 1.45
SiO2 = mp.Medium(index=nSiO2)
s = 1.0
cell_size = mp.Vector3(s, s, s)
rad = 0.34 # radius of sphere
if use_matgrid:
matgrid_resolution = 2 * resolution
N = int(s * matgrid_resolution)
coord = np.linspace(-0.5 * s, 0.5 * s, N)
xv, yv, zv = np.meshgrid(coord, coord, coord)
weights = np.sqrt(np.square(xv) + np.square(yv) + np.square(zv)) < rad
filtered_weights = gaussian_filter(weights,
sigma=4 / resolution,
output=np.double)
matgrid = mp.MaterialGrid(mp.Vector3(N, N, N),
SiO2,
Si,
weights=filtered_weights,
do_averaging=True,
beta=1000,
eta=0.5)
geometry = [
mp.Block(center=mp.Vector3(), size=cell_size, material=matgrid)
]
else:
geometry = [mp.Sphere(center=mp.Vector3(), radius=rad, material=Si)]
sources = [
mp.Source(src=mp.GaussianSource(fcen, fwidth=df),
size=mp.Vector3(),
center=mp.Vector3(0.13, 0.25, 0.06),
component=mp.Ez)
]
k_point = mp.Vector3(0.23, -0.17, 0.35)
sim = mp.Simulation(resolution=resolution,
cell_size=cell_size,
sources=sources,
default_material=SiO2,
k_point=k_point,
geometry=geometry)
h = mp.Harminv(mp.Ez, mp.Vector3(-0.2684, 0.1185, 0.0187), fcen, df)
sim.run(mp.after_sources(h), until_after_sources=200)
try:
for m in h.modes:
print("harminv:, {}, {}, {}".format(resolution, m.freq, m.Q))
freq = h.modes[0].freq
except:
raise RuntimeError("No resonant modes found.")
return freq
center=mp.Vector3(0, 0, -(sizeZ / 2 + 6 * addFlux)), #3D case
# center=mp.Vector3(-sizeX/2, 0, 0),
size=mp.Vector3(sizeX, sizeY, 0),
amplitude=1)
]
#sources = create_sources(freq, df, 0.7, 5, resolution, 4, 0, 0, 0, 24, 0)
#sys.stderr.write(np.str(mp.Vector3(z=-0.5*sizeZ-addFlux/2)))
#sys.stderr.write(np.str(mp.Vector3(sizeX+addFlux/2, sizeY+addFlux/2, 0)))
geometry = []
while Z < sizeZ / 2 - 1:
for i in range(N):
coord[0, i] = np.random.rand() * sizeX - sizeX / 2
coord[1, i] = np.random.rand() * sizeY - sizeY / 2
coord[2, i] = Z
bufferShape = mp.Sphere(center=mp.Vector3(coord[0, i], coord[1, i],
coord[2, i]),
radius=radius,
material=mp.Medium(epsilon=1.44))
geometry.append(bufferShape)
Z = Z + dZ
# for i in range(N):
# coord[0, i] = np.random.rand()*sizeX-sizeX/2
# coord[1, i] = np.random.rand()*sizeY-sizeY/2
# coord[2, i] = Z
# bufferShape = mp.Sphere(center=mp.Vector3(coord[0, i], coord[1, i], coord[2, i]),
# radius=radius,
# material=mp.Medium(epsilon=12))
# geometry.append(bufferShape)
pml_layers = [mp.PML(thicknessPML)]
sim = mp.Simulation(
cell_size=cell,
def main(from_um_factor, resolution, courant, r, material, paper, reference,
submerged_index, displacement, surface_index, wlen_range, nfreq,
air_r_factor, pml_wlen_factor, flux_r_factor, time_factor_cell,
second_time_factor, series, folder, parallel, n_processes, n_cores,
n_nodes, split_chunks_evenly, load_flux, load_chunks, near2far):
#%% CLASSIC INPUT PARAMETERS
"""
# Simulation size
from_um_factor = 10e-3 # Conversion of 1 μm to my length unit (=10nm/1μm)
resolution = 2 # >=8 pixels per smallest wavelength, i.e. np.floor(8/wvl_min)
courant = 0.5
# Nanoparticle specifications: Sphere in Vacuum :)
r = 51.5 # Radius of sphere in nm
paper = "R"
reference = "Meep"
displacement = 0 # Displacement of the surface from the bottom of the sphere in nm
submerged_index = 1 # 1.33 for water
surface_index = 1 # 1.54 for glass
# Frequency and wavelength
wlen_range = np.array([350,500]) # Wavelength range in nm
nfreq = 100
# Box dimensions
pml_wlen_factor = 0.38
air_r_factor = 0.5
flux_r_factor = 0 #0.1
# Simulation time
time_factor_cell = 1.2
second_time_factor = 10
# Saving directories
series = "SilverRes4"
folder = "Test/TestSilver"
# Configuration
parallel = False
n_processes = 1
n_cores = 1
n_nodes = 1
split_chunks_evenly = True
load_flux = False
load_chunks = True
near2far = False
"""
#%% MORE INPUT PARAMETERS
# Frequency and wavelength
cutoff = 3.2 # Gaussian planewave source's parameter of shape
nazimuthal = 16
npolar = 20
### TREATED INPUT PARAMETERS
# Nanoparticle specifications: Sphere in Vacuum :)
r = r / (from_um_factor * 1e3) # Now in Meep units
if reference == "Meep":
medium = vmt.import_medium(material,
from_um_factor=from_um_factor,
paper=paper)
# Importing material constants dependant on frequency from Meep Library
elif reference == "RIinfo":
medium = vmt.MediumFromFile(material,
paper=paper,
reference=reference,
from_um_factor=from_um_factor)
# Importing material constants dependant on frequency from external file
else:
raise ValueError("Reference for medium not recognized. Sorry :/")
displacement = displacement / (from_um_factor * 1e3) # Now in Meep units
# Frequency and wavelength
wlen_range = np.array(wlen_range)
wlen_range = wlen_range / (from_um_factor * 1e3) # Now in Meep units
freq_range = 1 / wlen_range # Hz range in Meep units from highest to lowest
freq_center = np.mean(freq_range)
freq_width = max(freq_range) - min(freq_range)
# Space configuration
pml_width = pml_wlen_factor * max(wlen_range) # 0.5 * max(wlen_range)
air_width = air_r_factor * r # 0.5 * max(wlen_range)
flux_box_size = 2 * (1 + flux_r_factor) * r
# Saving directories
if series is None:
series = "Test"
if folder is None:
folder = "Test"
params_list = [
"from_um_factor", "resolution", "courant", "material", "r", "paper",
"reference", "submerged_index", "displacement", "surface_index",
"wlen_range", "nfreq", "nazimuthal", "npolar", "cutoff",
"flux_box_size", "cell_width", "pml_width", "air_width",
"source_center", "until_after_sources", "time_factor_cell",
"second_time_factor", "enlapsed", "parallel", "n_processes", "n_cores",
"n_nodes", "split_chunks_evenly", "near2far", "script", "sysname",
"path"
]
#%% GENERAL GEOMETRY SETUP
air_width = air_width - air_width % (1 / resolution)
pml_width = pml_width - pml_width % (1 / resolution)
pml_layers = [mp.PML(thickness=pml_width)]
# symmetries = [mp.Mirror(mp.Y),
# mp.Mirror(mp.Z, phase=-1)]
# Two mirror planes reduce cell size to 1/4
# Issue related that lead me to comment this lines:
# https://github.com/NanoComp/meep/issues/1484
cell_width = 2 * (pml_width + air_width + r)
cell_width = cell_width - cell_width % (1 / resolution)
cell_size = mp.Vector3(cell_width, cell_width, cell_width)
# surface_center = r/4 - displacement/2 + cell_width/4
# surface_center = surface_center - surface_center%(1/resolution)
# displacement = r/2 + cell_width/2 - 2*surface_center
displacement = displacement - displacement % (1 / resolution)
flux_box_size = flux_box_size - flux_box_size % (1 / resolution)
source_center = -0.5 * cell_width + pml_width
sources = [
mp.Source(mp.GaussianSource(freq_center,
fwidth=freq_width,
is_integrated=True,
cutoff=cutoff),
center=mp.Vector3(source_center),
size=mp.Vector3(0, cell_width, cell_width),
component=mp.Ez)
]
# Ez-polarized planewave pulse
# (its size parameter fills the entire cell in 2d)
# >> The planewave source extends into the PML
# ==> is_integrated=True must be specified
until_after_sources = time_factor_cell * cell_width * submerged_index
# Enough time for the pulse to pass through all the cell
# Originally: Aprox 3 periods of lowest frequency, using T=λ/c=λ in Meep units
# Now: Aprox 3 periods of highest frequency, using T=λ/c=λ in Meep units
geometry = [mp.Sphere(material=medium, center=mp.Vector3(), radius=r)]
# Au sphere with frequency-dependant characteristics imported from Meep.
if surface_index != 1:
geometry = [
mp.Block(material=mp.Medium(index=surface_index),
center=mp.Vector3(
r / 2 - displacement / 2 + cell_width / 4, 0, 0),
size=mp.Vector3(cell_width / 2 - r + displacement,
cell_width, cell_width)), *geometry
]
# A certain material surface underneath it
home = vs.get_home()
sysname = vs.get_sys_name()
path = os.path.join(home, folder, series)
if not os.path.isdir(path) and vm.parallel_assign(0, n_processes,
parallel):
os.makedirs(path)
file = lambda f: os.path.join(path, f)
# Computation
enlapsed = []
parallel_specs = np.array([n_processes, n_cores, n_nodes], dtype=int)
max_index = np.argmax(parallel_specs)
for index, item in enumerate(parallel_specs):
if item == 0: parallel_specs[index] = 1
parallel_specs[0:max_index] = np.full(parallel_specs[0:max_index].shape,
max(parallel_specs))
n_processes, n_cores, n_nodes = parallel_specs
parallel = max(parallel_specs) > 1
del parallel_specs, max_index, index, item
if parallel:
np_process = mp.count_processors()
else:
np_process = 1
#%% FIRST RUN
measure_ram()
params = {}
for p in params_list:
params[p] = eval(p)
stable, max_courant = vm.check_stability(params)
if stable:
print("As a whole, the simulation should be stable")
else:
print("As a whole, the simulation could not be stable")
print(f"Recommended maximum courant factor is {max_courant}")
if load_flux:
try:
flux_path = vm.check_midflux(params)[0]
flux_needed = False
except:
flux_needed = True
else:
flux_needed = True
if load_chunks and not split_chunks_evenly:
try:
chunks_path = vm.check_chunks(params)[0]
chunk_layout = os.path.join(chunks_path, "Layout.h5")
chunks_needed = False
except:
chunks_needed = True
flux_needed = True
else:
if not split_chunks_evenly:
chunks_needed = True
flux_needed = True
else:
chunk_layout = None
chunks_needed = False
if chunks_needed:
sim = mp.Simulation(
resolution=resolution,
cell_size=cell_size,
boundary_layers=pml_layers,
sources=sources,
k_point=mp.Vector3(),
Courant=courant,
default_material=mp.Medium(index=submerged_index),
output_single_precision=True,
split_chunks_evenly=split_chunks_evenly,
# symmetries=symmetries,
geometry=geometry)
sim.init_sim()
chunks_path = vm.save_chunks(sim, params, path)
chunk_layout = os.path.join(chunks_path, "Layout.h5")
del sim
if flux_needed:
#% FIRST RUN: SET UP
measure_ram()
sim = mp.Simulation(resolution=resolution,
cell_size=cell_size,
boundary_layers=pml_layers,
sources=sources,
k_point=mp.Vector3(),
Courant=courant,
default_material=mp.Medium(index=submerged_index),
split_chunks_evenly=split_chunks_evenly,
chunk_layout=chunk_layout,
output_single_precision=True) #,
# symmetries=symmetries)
# >> k_point zero specifies boundary conditions needed
# for the source to be infinitely extended
measure_ram()
# Scattered power --> Computed by surrounding it with closed DFT flux box
# (its size and orientation are irrelevant because of Poynting's theorem)
box_x1 = sim.add_flux(
freq_center, freq_width, nfreq,
mp.FluxRegion(center=mp.Vector3(x=-flux_box_size / 2),
size=mp.Vector3(0, flux_box_size, flux_box_size)))
box_x2 = sim.add_flux(
freq_center, freq_width, nfreq,
mp.FluxRegion(center=mp.Vector3(x=+flux_box_size / 2),
size=mp.Vector3(0, flux_box_size, flux_box_size)))
box_y1 = sim.add_flux(
freq_center, freq_width, nfreq,
mp.FluxRegion(center=mp.Vector3(y=-flux_box_size / 2),
size=mp.Vector3(flux_box_size, 0, flux_box_size)))
box_y2 = sim.add_flux(
freq_center, freq_width, nfreq,
mp.FluxRegion(center=mp.Vector3(y=+flux_box_size / 2),
size=mp.Vector3(flux_box_size, 0, flux_box_size)))
box_z1 = sim.add_flux(
freq_center, freq_width, nfreq,
mp.FluxRegion(center=mp.Vector3(z=-flux_box_size / 2),
size=mp.Vector3(flux_box_size, flux_box_size, 0)))
box_z2 = sim.add_flux(
freq_center, freq_width, nfreq,
mp.FluxRegion(center=mp.Vector3(z=+flux_box_size / 2),
size=mp.Vector3(flux_box_size, flux_box_size, 0)))
# Funny you can encase the sphere (r radius) so closely (2r-sided box)
measure_ram()
if near2far:
near2far_box = sim.add_near2far(
freq_center, freq_width, nfreq,
mp.Near2FarRegion(center=mp.Vector3(x=-flux_box_size / 2),
size=mp.Vector3(0, flux_box_size,
flux_box_size),
weight=-1),
mp.Near2FarRegion(center=mp.Vector3(x=+flux_box_size / 2),
size=mp.Vector3(0, flux_box_size,
flux_box_size),
weight=+1),
mp.Near2FarRegion(center=mp.Vector3(y=-flux_box_size / 2),
size=mp.Vector3(flux_box_size, 0,
flux_box_size),
weight=-1),
mp.Near2FarRegion(center=mp.Vector3(y=+flux_box_size / 2),
size=mp.Vector3(flux_box_size, 0,
flux_box_size),
weight=+1),
mp.Near2FarRegion(center=mp.Vector3(z=-flux_box_size / 2),
size=mp.Vector3(flux_box_size, flux_box_size,
0),
weight=-1),
mp.Near2FarRegion(center=mp.Vector3(z=+flux_box_size / 2),
size=mp.Vector3(flux_box_size, flux_box_size,
0),
weight=+1))
measure_ram()
else:
near2far_box = None
# used_ram.append(used_ram[-1])
#% FIRST RUN: INITIALIZE
temp = time()
sim.init_sim()
enlapsed.append(time() - temp)
measure_ram()
step_ram_function = lambda sim: measure_ram()
#% FIRST RUN: SIMULATION NEEDED TO NORMALIZE
temp = time()
sim.run(mp.at_beginning(step_ram_function),
mp.at_time(int(until_after_sources / 2), step_ram_function),
mp.at_end(step_ram_function),
until_after_sources=until_after_sources)
# mp.stop_when_fields_decayed(
# np.mean(wlen_range), # dT = mean period of source
# mp.Ez, # Component of field to check
# mp.Vector3(0.5*cell_width - pml_width, 0, 0), # Where to check
# 1e-3)) # Factor to decay
enlapsed.append(time() - temp)
#% SAVE MID DATA
for p in params_list:
params[p] = eval(p)
flux_path = vm.save_midflux(sim, box_x1, box_x2, box_y1, box_y2,
box_z1, box_z2, near2far_box, params, path)
freqs = np.asarray(mp.get_flux_freqs(box_x1))
box_x1_flux0 = np.asarray(mp.get_fluxes(box_x1))
box_x2_flux0 = np.asarray(mp.get_fluxes(box_x2))
box_y1_flux0 = np.asarray(mp.get_fluxes(box_y1))
box_y2_flux0 = np.asarray(mp.get_fluxes(box_y2))
box_z1_flux0 = np.asarray(mp.get_fluxes(box_z1))
box_z2_flux0 = np.asarray(mp.get_fluxes(box_z2))
data_mid = np.array([
1e3 * from_um_factor / freqs, box_x1_flux0, box_x2_flux0,
box_y1_flux0, box_y2_flux0, box_z1_flux0, box_z2_flux0
]).T
header_mid = [
"Longitud de onda [nm]", "Flujo X10 [u.a.]", "Flujo X20 [u.a]",
"Flujo Y10 [u.a]", "Flujo Y20 [u.a]", "Flujo Z10 [u.a]",
"Flujo Z20 [u.a]"
]
if vm.parallel_assign(0, n_processes, parallel):
vs.savetxt(file("MidFlux.txt"),
data_mid,
header=header_mid,
footer=params)
if not split_chunks_evenly:
vm.save_chunks(sim, params, path)
if parallel:
f = h5.File(file("MidRAM.h5"),
"w",
driver='mpio',
comm=MPI.COMM_WORLD)
current_process = mp.my_rank()
f.create_dataset("RAM", (len(used_ram), np_process), dtype="float")
f["RAM"][:, current_process] = used_ram
for a in params:
f["RAM"].attrs[a] = params[a]
f.create_dataset("SWAP", (len(used_ram), np_process), dtype="int")
f["SWAP"][:, current_process] = swapped_ram
for a in params:
f["SWAP"].attrs[a] = params[a]
else:
f = h5.File(file("MidRAM.h5"), "w")
f.create_dataset("RAM", data=used_ram)
for a in params:
f["RAM"].attrs[a] = params[a]
f.create_dataset("SWAP", data=swapped_ram)
for a in params:
f["SWAP"].attrs[a] = params[a]
f.close()
del f
#% PLOT FLUX FOURIER MID DATA
if vm.parallel_assign(1, np_process, parallel):
ylims = (np.min(data_mid[:, 1:]), np.max(data_mid[:, 1:]))
ylims = (ylims[0] - .1 * (ylims[1] - ylims[0]),
ylims[1] + .1 * (ylims[1] - ylims[0]))
fig, ax = plt.subplots(3, 2, sharex=True)
fig.subplots_adjust(hspace=0, wspace=.05)
for a in ax[:, 1]:
a.yaxis.tick_right()
a.yaxis.set_label_position("right")
for a, h in zip(np.reshape(ax, 6), header_mid[1:]):
a.set_ylabel(h)
for d, a in zip(data_mid[:, 1:].T, np.reshape(ax, 6)):
a.plot(1e3 * from_um_factor / freqs, d)
a.set_ylim(*ylims)
ax[-1, 0].set_xlabel("Wavelength [nm]")
ax[-1, 1].set_xlabel("Wavelength [nm]")
plt.savefig(file("MidFlux.png"))
del fig, ax, ylims, a, h
sim.reset_meep()
#%% SECOND RUN: SETUP
measure_ram()
sim = mp.Simulation(
resolution=resolution,
cell_size=cell_size,
boundary_layers=pml_layers,
sources=sources,
k_point=mp.Vector3(),
Courant=courant,
default_material=mp.Medium(index=submerged_index),
output_single_precision=True,
split_chunks_evenly=split_chunks_evenly,
chunk_layout=chunk_layout,
# symmetries=symmetries,
geometry=geometry)
measure_ram()
box_x1 = sim.add_flux(
freq_center, freq_width, nfreq,
mp.FluxRegion(center=mp.Vector3(x=-flux_box_size / 2),
size=mp.Vector3(0, flux_box_size, flux_box_size)))
box_x2 = sim.add_flux(
freq_center, freq_width, nfreq,
mp.FluxRegion(center=mp.Vector3(x=+flux_box_size / 2),
size=mp.Vector3(0, flux_box_size, flux_box_size)))
box_y1 = sim.add_flux(
freq_center, freq_width, nfreq,
mp.FluxRegion(center=mp.Vector3(y=-flux_box_size / 2),
size=mp.Vector3(flux_box_size, 0, flux_box_size)))
box_y2 = sim.add_flux(
freq_center, freq_width, nfreq,
mp.FluxRegion(center=mp.Vector3(y=+flux_box_size / 2),
size=mp.Vector3(flux_box_size, 0, flux_box_size)))
box_z1 = sim.add_flux(
freq_center, freq_width, nfreq,
mp.FluxRegion(center=mp.Vector3(z=-flux_box_size / 2),
size=mp.Vector3(flux_box_size, flux_box_size, 0)))
box_z2 = sim.add_flux(
freq_center, freq_width, nfreq,
mp.FluxRegion(center=mp.Vector3(z=+flux_box_size / 2),
size=mp.Vector3(flux_box_size, flux_box_size, 0)))
measure_ram()
if near2far:
near2far_box = sim.add_near2far(
freq_center, freq_width, nfreq,
mp.Near2FarRegion(center=mp.Vector3(x=-flux_box_size / 2),
size=mp.Vector3(0, flux_box_size, flux_box_size),
weight=-1),
mp.Near2FarRegion(center=mp.Vector3(x=+flux_box_size / 2),
size=mp.Vector3(0, flux_box_size, flux_box_size),
weight=+1),
mp.Near2FarRegion(center=mp.Vector3(y=-flux_box_size / 2),
size=mp.Vector3(flux_box_size, 0, flux_box_size),
weight=-1),
mp.Near2FarRegion(center=mp.Vector3(y=+flux_box_size / 2),
size=mp.Vector3(flux_box_size, 0, flux_box_size),
weight=+1),
mp.Near2FarRegion(center=mp.Vector3(z=-flux_box_size / 2),
size=mp.Vector3(flux_box_size, flux_box_size, 0),
weight=-1),
mp.Near2FarRegion(center=mp.Vector3(z=+flux_box_size / 2),
size=mp.Vector3(flux_box_size, flux_box_size, 0),
weight=+1))
measure_ram()
else:
near2far_box = None
# used_ram.append(used_ram[-1])
#%% SECOND RUN: INITIALIZE
temp = time()
sim.init_sim()
enlapsed.append(time() - temp)
measure_ram()
#%% LOAD FLUX FROM FILE
vm.load_midflux(sim, box_x1, box_x2, box_y1, box_y2, box_z1, box_z2,
near2far_box, flux_path)
measure_ram()
freqs = np.asarray(mp.get_flux_freqs(box_x1))
box_x1_flux0 = np.asarray(mp.get_fluxes(box_x1))
box_x1_data = sim.get_flux_data(box_x1)
box_x2_data = sim.get_flux_data(box_x2)
box_y1_data = sim.get_flux_data(box_y1)
box_y2_data = sim.get_flux_data(box_y2)
box_z1_data = sim.get_flux_data(box_z1)
box_z2_data = sim.get_flux_data(box_z2)
if near2far: near2far_data = sim.get_near2far_data(near2far_box)
temp = time()
sim.load_minus_flux_data(box_x1, box_x1_data)
sim.load_minus_flux_data(box_x2, box_x2_data)
sim.load_minus_flux_data(box_y1, box_y1_data)
sim.load_minus_flux_data(box_y2, box_y2_data)
sim.load_minus_flux_data(box_z1, box_z1_data)
sim.load_minus_flux_data(box_z2, box_z2_data)
if near2far: sim.load_minus_near2far_data(near2far_box, near2far_data)
enlapsed.append(time() - temp)
del box_x1_data, box_x2_data, box_y1_data, box_y2_data
del box_z1_data, box_z2_data
if near2far: del near2far_data
measure_ram()
#%% SECOND RUN: SIMULATION :D
step_ram_function = lambda sim: measure_ram()
temp = time()
sim.run(mp.at_beginning(step_ram_function),
mp.at_time(int(second_time_factor * until_after_sources / 2),
step_ram_function),
mp.at_end(step_ram_function),
until_after_sources=second_time_factor * until_after_sources)
# mp.stop_when_fields_decayed(
# np.mean(wlen_range), # dT = mean period of source
# mp.Ez, # Component of field to check
# mp.Vector3(0.5*cell_width - pml_width, 0, 0), # Where to check
# 1e-3)) # Factor to decay
enlapsed.append(time() - temp)
del temp
# Aprox 30 periods of lowest frequency, using T=λ/c=λ in Meep units
box_x1_flux = np.asarray(mp.get_fluxes(box_x1))
box_x2_flux = np.asarray(mp.get_fluxes(box_x2))
box_y1_flux = np.asarray(mp.get_fluxes(box_y1))
box_y2_flux = np.asarray(mp.get_fluxes(box_y2))
box_z1_flux = np.asarray(mp.get_fluxes(box_z1))
box_z2_flux = np.asarray(mp.get_fluxes(box_z2))
#%% SCATTERING ANALYSIS
scatt_flux = box_x1_flux - box_x2_flux
scatt_flux = scatt_flux + box_y1_flux - box_y2_flux
scatt_flux = scatt_flux + box_z1_flux - box_z2_flux
intensity = box_x1_flux0 / (flux_box_size)**2
# Flux of one of the six monitor planes / Área
# (the closest one, facing the planewave source)
# This is why the six sides of the flux box are separated
# (Otherwise, the box could've been one flux object with weights ±1 per side)
scatt_cross_section = np.divide(scatt_flux, intensity)
# Scattering cross section σ =
# = scattered power in all directions / incident intensity.
scatt_eff_meep = -1 * scatt_cross_section / (np.pi * r**2)
# Scattering efficiency =
# = scattering cross section / cross sectional area of the sphere
freqs = np.array(freqs)
scatt_eff_theory = [
ps.MieQ(np.sqrt(medium.epsilon(f)[0, 0] * medium.mu(f)[0, 0]),
1e3 * from_um_factor / f,
2 * r * 1e3 * from_um_factor,
nMedium=submerged_index,
asDict=True)['Qsca'] for f in freqs
]
# The simulation results are validated by comparing with
# analytic theory of PyMieScatt module
#%% ANGULAR PATTERN ANALYSIS
if near2far:
fraunhofer_distance = 8 * (r**2) / min(wlen_range)
radial_distance = max(10 * fraunhofer_distance, 1.5 * cell_width / 2)
# radius of far-field circle must be at least Fraunhofer distance
azimuthal_angle = np.arange(0, 2 + 2 / nazimuthal,
2 / nazimuthal) # in multiples of pi
polar_angle = np.arange(0, 1 + 1 / npolar, 1 / npolar)
poynting_x = []
poynting_y = []
poynting_z = []
poynting_r = []
for phi in azimuthal_angle:
poynting_x.append([])
poynting_y.append([])
poynting_z.append([])
poynting_r.append([])
for theta in polar_angle:
farfield_dict = sim.get_farfields(
near2far_box,
1,
where=mp.Volume(center=mp.Vector3(
radial_distance * np.cos(np.pi * phi) *
np.sin(np.pi * theta),
radial_distance * np.sin(np.pi * phi) *
np.sin(np.pi *
theta), radial_distance *
np.cos(np.pi * theta))))
Px = farfield_dict["Ey"] * np.conjugate(farfield_dict["Hz"])
Px -= farfield_dict["Ez"] * np.conjugate(farfield_dict["Hy"])
Py = farfield_dict["Ez"] * np.conjugate(farfield_dict["Hx"])
Py -= farfield_dict["Ex"] * np.conjugate(farfield_dict["Hz"])
Pz = farfield_dict["Ex"] * np.conjugate(farfield_dict["Hy"])
Pz -= farfield_dict["Ey"] * np.conjugate(farfield_dict["Hx"])
Px = np.real(Px)
Py = np.real(Py)
Pz = np.real(Pz)
poynting_x[-1].append(Px)
poynting_y[-1].append(Py)
poynting_z[-1].append(Pz)
poynting_r[-1].append(
np.sqrt(np.square(Px) + np.square(Py) + np.square(Pz)))
poynting_x = np.array(poynting_x)
poynting_y = np.array(poynting_y)
poynting_z = np.array(poynting_z)
poynting_r = np.array(poynting_r)
#%% SAVE FINAL DATA
for p in params_list:
params[p] = eval(p)
data = np.array(
[1e3 * from_um_factor / freqs, scatt_eff_meep, scatt_eff_theory]).T
header = [
"Longitud de onda [nm]", "Sección eficaz efectiva (Meep) [u.a.]",
"Sección eficaz efectiva (Theory) [u.a.]"
]
data_base = np.array([
1e3 * from_um_factor / freqs, box_x1_flux0, box_x1_flux, box_x2_flux,
box_y1_flux, box_y2_flux, box_z1_flux, box_z2_flux, intensity,
scatt_flux, scatt_cross_section
]).T
header_base = [
"Longitud de onda [nm]", "Flujo X10 [u.a.]", "Flujo X1 [u.a]",
"Flujo X2 [u.a]", "Flujo Y1 [u.a]", "Flujo Y2 [u.a]", "Flujo Z1 [u.a]",
"Flujo Z2 [u.a]", "Intensidad incidente [u.a.]",
"Flujo scattereado [u.a.]", "Sección eficaz de scattering [u.a.]"
]
if vm.parallel_assign(0, np_process, parallel):
vs.savetxt(file("Results.txt"), data, header=header, footer=params)
vs.savetxt(file("BaseResults.txt"),
data_base,
header=header_base,
footer=params)
if near2far:
header_near2far = [
"Poynting medio Px [u.a.]", "Poynting medio Py [u.a.]",
"Poynting medio Pz [u.a.]", "Poynting medio Pr [u.a.]"
]
data_near2far = [
poynting_x.reshape(poynting_x.size),
poynting_y.reshape(poynting_y.size),
poynting_z.reshape(poynting_z.size),
poynting_r.reshape(poynting_r.size)
]
if vm.parallel_assign(1, np_process, parallel):
vs.savetxt(file("Near2FarResults.txt"),
data_near2far,
header=header_near2far,
footer=params)
if not split_chunks_evenly:
vm.save_chunks(sim, params, path)
if parallel:
f = h5.File(file("RAM.h5"), "w", driver='mpio', comm=MPI.COMM_WORLD)
current_process = mp.my_rank()
f.create_dataset("RAM", (len(used_ram), np_process), dtype="float")
f["RAM"][:, current_process] = used_ram
for a in params:
f["RAM"].attrs[a] = params[a]
f.create_dataset("SWAP", (len(used_ram), np_process), dtype="int")
f["SWAP"][:, current_process] = swapped_ram
for a in params:
f["SWAP"].attrs[a] = params[a]
else:
f = h5.File(file("RAM.h5"), "w")
f.create_dataset("RAM", data=used_ram)
for a in params:
f["RAM"].attrs[a] = params[a]
f.create_dataset("SWAP", data=swapped_ram)
for a in params:
f["SWAP"].attrs[a] = params[a]
f.close()
del f
if flux_needed and vm.parallel_assign(0, np_process, parallel):
os.remove(file("MidRAM.h5"))
#%% PLOT ALL TOGETHER
if vm.parallel_assign(0, np_process, parallel) and surface_index == 1:
plt.figure()
plt.plot(1e3 * from_um_factor / freqs,
scatt_eff_meep,
'bo-',
label='Meep')
plt.plot(1e3 * from_um_factor / freqs,
scatt_eff_theory,
'ro-',
label='Theory')
plt.xlabel('Wavelength [nm]')
plt.ylabel('Scattering efficiency [σ/πr$^{2}$]')
plt.legend()
plt.title('Scattering of Au Sphere With {:.1f} nm Radius'.format(
r * from_um_factor * 1e3))
plt.tight_layout()
plt.savefig(file("Comparison.png"))
#%% PLOT SEPARATE
if vm.parallel_assign(1, np_process, parallel):
plt.figure()
plt.plot(1e3 * from_um_factor / freqs,
scatt_eff_meep,
'bo-',
label='Meep')
plt.xlabel('Wavelength [nm]')
plt.ylabel('Scattering efficiency [σ/πr$^{2}$]')
plt.legend()
plt.title('Scattering of Au Sphere With {:.1f} nm Radius'.format(
r * from_um_factor * 1e3))
plt.tight_layout()
plt.savefig(file("Meep.png"))
if vm.parallel_assign(0, np_process, parallel) and surface_index == 1:
plt.figure()
plt.plot(1e3 * from_um_factor / freqs,
scatt_eff_theory,
'ro-',
label='Theory')
plt.xlabel('Wavelength [nm]')
plt.ylabel('Scattering efficiency [σ/πr$^{2}$]')
plt.legend()
plt.title('Scattering of Au Sphere With {:.1f} nm Radius'.format(r *
10))
plt.tight_layout()
plt.savefig(file("Theory.png"))
#%% PLOT ONE ABOVE THE OTHER
if vm.parallel_assign(1, np_process, parallel) and surface_index == 1:
fig, axes = plt.subplots(nrows=2, sharex=True)
fig.subplots_adjust(hspace=0)
plt.suptitle('Scattering of Au Sphere With {:.1f} nm Radius'.format(
r * from_um_factor * 1e3))
axes[0].plot(1e3 * from_um_factor / freqs,
scatt_eff_meep,
'bo-',
label='Meep')
axes[0].yaxis.tick_right()
axes[0].set_ylabel('Scattering efficiency [σ/πr$^{2}$]')
axes[0].legend()
axes[1].plot(1e3 * from_um_factor / freqs,
scatt_eff_theory,
'ro-',
label='Theory')
axes[1].set_xlabel('Wavelength [nm]')
axes[1].set_ylabel('Scattering efficiency [σ/πr$^{2}$]')
axes[1].legend()
plt.savefig(file("SeparatedComparison.png"))
#%% PLOT FLUX FOURIER FINAL DATA
if vm.parallel_assign(0, np_process, parallel):
ylims = (np.min(data_base[:, 2:8]), np.max(data_base[:, 2:8]))
ylims = (ylims[0] - .1 * (ylims[1] - ylims[0]),
ylims[1] + .1 * (ylims[1] - ylims[0]))
fig, ax = plt.subplots(3, 2, sharex=True)
fig.subplots_adjust(hspace=0, wspace=.05)
plt.suptitle('Final flux of Au Sphere With {:.1f} nm Radius'.format(
r * from_um_factor * 1e3))
for a in ax[:, 1]:
a.yaxis.tick_right()
a.yaxis.set_label_position("right")
for a, h in zip(np.reshape(ax, 6), header_base[1:7]):
a.set_ylabel(h)
for d, a in zip(data_base[:, 3:9].T, np.reshape(ax, 6)):
a.plot(1e3 * from_um_factor / freqs, d)
a.set_ylim(*ylims)
ax[-1, 0].set_xlabel("Wavelength [nm]")
ax[-1, 1].set_xlabel("Wavelength [nm]")
plt.savefig(file("FinalFlux.png"))
#%% PLOT ANGULAR PATTERN IN 3D
if near2far and vm.parallel_assign(1, np_process, parallel):
freq_index = np.argmin(np.abs(freqs - freq_center))
fig = plt.figure()
plt.suptitle(
'Angular Pattern of Au Sphere With {:.1f} nm Radius at {:.1f} nm'.
format(r * from_um_factor * 1e3,
from_um_factor * 1e3 / freqs[freq_index]))
ax = fig.add_subplot(1, 1, 1, projection='3d')
ax.plot_surface(poynting_x[:, :, freq_index],
poynting_y[:, :, freq_index],
poynting_z[:, :, freq_index],
cmap=plt.get_cmap('jet'),
linewidth=1,
antialiased=False,
alpha=0.5)
ax.set_xlabel(r"$P_x$")
ax.set_ylabel(r"$P_y$")
ax.set_zlabel(r"$P_z$")
plt.savefig(file("AngularPattern.png"))
#%% PLOT ANGULAR PATTERN PROFILE FOR DIFFERENT POLAR ANGLES
if near2far and vm.parallel_assign(0, np_process, parallel):
freq_index = np.argmin(np.abs(freqs - freq_center))
index = [
list(polar_angle).index(alpha) for alpha in [0, .25, .5, .75, 1]
]
plt.figure()
plt.suptitle(
'Angular Pattern of Au Sphere With {:.1f} nm Radius at {:.1f} nm'.
format(r * from_um_factor * 1e3,
from_um_factor * 1e3 / freqs[freq_index]))
ax_plain = plt.axes()
for i in index:
ax_plain.plot(poynting_x[:, i, freq_index],
poynting_y[:, i, freq_index],
".-",
label=rf"$\theta$ = {polar_angle[i]:.2f} $\pi$")
plt.legend()
ax_plain.set_xlabel(r"$P_x$")
ax_plain.set_ylabel(r"$P_y$")
ax_plain.set_aspect("equal")
plt.savefig(file("AngularPolar.png"))
#%% PLOT ANGULAR PATTERN PROFILE FOR DIFFERENT AZIMUTHAL ANGLES
if near2far and vm.parallel_assign(1, np_process, parallel):
freq_index = np.argmin(np.abs(freqs - freq_center))
index = [
list(azimuthal_angle).index(alpha)
for alpha in [0, .25, .5, .75, 1, 1.25, 1.5, 1.75, 2]
]
plt.figure()
plt.suptitle(
'Angular Pattern of Au Sphere With {:.1f} nm Radius at {:.1f} nm'.
format(r * from_um_factor * 1e3,
from_um_factor * 1e3 / freqs[freq_index]))
ax_plain = plt.axes()
for i in index:
ax_plain.plot(poynting_x[i, :, freq_index],
poynting_z[i, :, freq_index],
".-",
label=rf"$\phi$ = {azimuthal_angle[i]:.2f} $\pi$")
plt.legend()
ax_plain.set_xlabel(r"$P_x$")
ax_plain.set_ylabel(r"$P_z$")
plt.savefig(file("AngularAzimuthal.png"))
if near2far and vm.parallel_assign(0, np_process, parallel):
freq_index = np.argmin(np.abs(freqs - freq_center))
index = [
list(azimuthal_angle).index(alpha)
for alpha in [0, .25, .5, .75, 1, 1.25, 1.5, 1.75, 2]
]
plt.figure()
plt.suptitle(
'Angular Pattern of Au Sphere With {:.1f} nm Radius at {:.1f} nm'.
format(r * from_um_factor * 1e3,
from_um_factor * 1e3 / freqs[freq_index]))
ax_plain = plt.axes()
for i in index:
ax_plain.plot(np.sqrt(
np.square(poynting_x[i, :, freq_index]) +
np.square(poynting_y[i, :, freq_index])),
poynting_z[i, :, freq_index],
".-",
label=rf"$\phi$ = {azimuthal_angle[i]:.2f} $\pi$")
plt.legend()
ax_plain.set_xlabel(r"$P_\rho$")
ax_plain.set_ylabel(r"$P_z$")
plt.savefig(file("AngularAzimuthalAbs.png"))
weight=+1),
mp.Near2FarRegion(center=mp.Vector3(z=+2 * r),
size=mp.Vector3(4 * r, 4 * r, 0),
weight=-1))
sim.run(until_after_sources=10)
input_flux = mp.get_fluxes(box_flux)[0]
nearfield_box_data = sim.get_near2far_data(nearfield_box)
sim.reset_meep()
n_sphere = 2.0
geometry = [
mp.Sphere(material=mp.Medium(index=n_sphere),
center=mp.Vector3(),
radius=r)
]
sim = mp.Simulation(resolution=resolution,
cell_size=cell_size,
boundary_layers=pml_layers,
sources=sources,
k_point=mp.Vector3(),
geometry=geometry)
nearfield_box = sim.add_near2far(
frq_cen, 0, 1,
mp.Near2FarRegion(center=mp.Vector3(x=-2 * r),
size=mp.Vector3(0, 4 * r, 4 * r),
weight=+1),
import meep as mp
import numpy as np
import matplotlib.pyplot as plt
import argparse
from meep.materials import Ag, BK7
sx = 4.0 #spatial extent along x including pmls (μm)
sy = 4.0
sz = 0.0
dpml = 1.0
cell = mp.Vector3(sx, sy, sz)
pml_layers = [mp.PML(dpml)]
geometry = [
mp.Sphere(radius=0.7, center=mp.Vector3(0, 0, 0), material=Ag),
mp.Sphere(radius=0.5,
center=mp.Vector3(0, 0, 0),
material=mp.Medium(epsilon=12.25))
]
resolution = 200
wvl = 825 / 1000 #convert args.wvl from nm to μm
fcen = 1 / wvl
df = 0
nfreq = 1
print("wavelength =", wvl, "μm")
print("center frequency =", fcen, "1/μm")
source = [
mp.Source(mp.GaussianSource(fcen, df, nfreq),
component=mp.Ey,
center=mp.Vector3(0, -0.705, 0))
cell_size = mp.Vector3(cell_width, cell_width, cell_width)
source_center = -0.5 * cell_width + pml_width
print("Resto Source Center: {}".format(source_center % (1 / resolution)))
sources = [
mp.Source(mp.ContinuousSource(wavelength=wlen, is_integrated=True),
center=mp.Vector3(source_center),
size=mp.Vector3(0, cell_width, cell_width),
component=mp.Ez)
]
# Ez-polarized monochromatic planewave
# (its size parameter fills the entire cell in 2d)
# >> The planewave source extends into the PML
# ==> is_integrated=True must be specified
geometry = [mp.Sphere(material=medium, center=mp.Vector3(), radius=r)]
# Au sphere with frequency-dependant characteristics imported from Meep.
path = os.path.join(home, folder, series)
if not os.path.isdir(path): vs.new_dir(path)
file = lambda f: os.path.join(path, f)
#%% SAVE GET FUNCTIONS
def get_line(sim):
return sim.get_array(center=mp.Vector3(),
size=mp.Vector3(cell_width),
component=mp.Ez)
def simulate(self, config):
start = time.time()
dpml = config["dpml"]
resolution = config["resolution"]
use_fixed_time = config["use_fixed_time"]
simulation_time = config["simulation_time"]
padding = config["padding"]
ff_pts = config["ff_pts"]
ff_cover = config["ff_cover"]
ff_calc = config["ff_calc"]
use_symmetries = config["use_symmetries"]
calculate_flux = config["calculate_flux"]
calculate_source_flux = config["calculate_source_flux"]
pixels = config["source_flux_pixel_size"]
ff_calculations = config["ff_calculations"]
ff_angle = math.pi / config["ff_angle"]
FibonacciSampling = config["fibb_sampling"]
simulation_ratio = eval(config["simulation_ratio"])
substrate_ratio = eval(config["substrate_ratio"])
output_ff = config["output_ff"]
polarization_in_plane = config["polarization_in_plane"]
geometry = config["geometry"]
material_function = config["material_function"]
substrate_height = self.pyramid_height * substrate_ratio #height of the substrate, measured as fraction of pyramid height
#"Cell size"
sx = self.pyramid_width * simulation_ratio #size of the cell in xy-plane is measured as a fraction of pyramid width
sy = sx
sz = self.pyramid_height * simulation_ratio #z-"height" of sim. cell measured as a fraction of pyramid height.
sh = substrate_height
sh = 0
padding = padding ##distance from pml_layers to flux regions so PML don't overlap flux regions
cell = mp.Vector3(sx + 2 * dpml, sy + 2 * dpml, sz +
2 * dpml) #size of the simulation cell in meep units
if self.CL_material == "Au":
CL_material = Au
elif self.CL_material == "Ag":
CL_material = Ag
elif self.CL_material == "Ag_visible":
CL_material = Ag_visible
else:
CL_material = GaN
print('CL MATERIAL:', CL_material, self.CL_material)
#Symmetries for the simulation
def create_symmetry(self):
if self.source_direction == mp.Ex or self.source_direction == [
1, 0, 0
]:
symmetry = [mp.Mirror(mp.Y), mp.Mirror(mp.X, phase=-1)]
elif self.source_direction == mp.Ey or self.source_direction == [
0, 1, 0
]:
symmetry = [mp.Mirror(mp.X), mp.Mirror(mp.Y, phase=-1)]
elif self.source_direction == mp.Ez or self.source_direction == [
0, 0, 1
]:
symmetry = [mp.Mirror(mp.X), mp.Mirror(mp.Y)]
else:
symmetry = []
return symmetry
#Flux regions to calculate the total flux emitted from the simulation
def define_flux_regions(sx, sy, sz, padding):
fluxregion = []
fluxregion.append(
mp.FluxRegion( #region x to calculate flux from
center=mp.Vector3(sx / 2 - padding, 0, 0),
size=mp.Vector3(0, sy - padding * 2, sz - padding * 2),
direction=mp.X))
fluxregion.append(
mp.FluxRegion( # region -x to calculate flux from
center=mp.Vector3(-sx / 2 + padding, 0, 0),
size=mp.Vector3(0, sy - padding * 2, sz - padding * 2),
direction=mp.X,
weight=-1))
fluxregion.append(
mp.FluxRegion( #region y to calculate flux from
center=mp.Vector3(0, sy / 2 - padding, 0),
size=mp.Vector3(sx - padding * 2, 0, sz - padding * 2),
direction=mp.Y))
fluxregion.append(
mp.FluxRegion( #region -y to calculate flux from
center=mp.Vector3(0, -sy / 2 + padding, 0),
size=mp.Vector3(sx - padding * 2, 0, sz - padding * 2),
direction=mp.Y,
weight=-1))
fluxregion.append(
mp.FluxRegion( #z-bottom region to calculate flux from
center=mp.Vector3(0, 0, sz / 2 - padding),
size=mp.Vector3(sx - padding * 2, sy - padding * 2, 0),
direction=mp.Z))
fluxregion.append(
mp.FluxRegion( #z-top region to calculate flux from
center=mp.Vector3(0, 0, -sz / 2 + padding),
size=mp.Vector3(sx - padding * 2, sy - padding * 2, 0),
direction=mp.Z,
weight=-1))
return fluxregion
#Flux regions to calculate the far field flux
def define_nearfield_regions(sx, sy, sz, sh, padding, ff_cover):
nearfieldregions = []
nfrAbove = []
nfrBelow = []
#if ff_calc == True:
#If we wish to calculate the far-field above and below the pyramid
# if ff_calc == "Both":
nfrAbove.append(
mp.Near2FarRegion(center=mp.Vector3(sx / 2 - padding, 0,
-sh / 2),
size=mp.Vector3(0, sy - padding * 2,
sz - sh - padding * 2),
direction=mp.X))
nfrAbove.append(
mp.Near2FarRegion(center=mp.Vector3(-sx / 2 + padding, 0,
-sh / 2),
size=mp.Vector3(0, sy - padding * 2,
sz - sh - padding * 2),
direction=mp.X,
weight=-1))
nfrAbove.append(
mp.Near2FarRegion(center=mp.Vector3(0, sy / 2 - padding,
-sh / 2),
size=mp.Vector3(sx - padding * 2, 0,
sz - sh - padding * 2),
direction=mp.Y))
nfrAbove.append(
mp.Near2FarRegion(center=mp.Vector3(0, -sy / 2 + padding,
-sh / 2),
size=mp.Vector3(sx - padding * 2, 0,
sz - sh - padding * 2),
direction=mp.Y,
weight=-1))
nfrAbove.append(
mp.Near2FarRegion( #nearfield -z. above pyramid.
center=mp.Vector3(0, 0, -sz / 2 + padding),
size=mp.Vector3(sx - padding * 2, sy - padding * 2, 0),
direction=mp.Z,
weight=-1))
#Far-field to calculate below transmissions
nfrBelow.append(
mp.Near2FarRegion(center=mp.Vector3(sx / 2 - padding, 0,
sz / 2 - sh / 2),
size=mp.Vector3(0, sy - padding * 2,
sh - padding * 2),
direction=mp.X))
nfrBelow.append(
mp.Near2FarRegion(center=mp.Vector3(-sx / 2 + padding, 0,
sz / 2 - sh / 2),
size=mp.Vector3(0, sy - padding * 2,
sh - padding * 2),
direction=mp.X,
weight=-1))
nfrBelow.append(
mp.Near2FarRegion(center=mp.Vector3(0, sy / 2 - padding,
sz / 2 - sh / 2),
size=mp.Vector3(sx - padding * 2, 0,
sh - padding * 2),
direction=mp.Y))
nfrBelow.append(
mp.Near2FarRegion(center=mp.Vector3(0, -sy / 2 + padding,
sz / 2 - sh / 2),
size=mp.Vector3(sx - padding * 2, 0,
sh - padding * 2),
direction=mp.Y,
weight=-1))
nfrBelow.append(
mp.Near2FarRegion(center=mp.Vector3(0, 0, sz / 2 - padding),
size=mp.Vector3(sx - padding * 2,
sy - padding * 2, 0),
direction=mp.Z))
if ff_cover == True:
nfrAbove.append(
mp.Near2FarRegion(center=mp.Vector3(
0, 0, sz / 2 - padding),
size=mp.Vector3(sx - padding * 2,
sy - padding * 2, 0),
direction=mp.Z))
nfrBelow.append(
mp.Near2FarRegion(center=mp.Vector3(
0, 0, -sz / 2 - padding),
size=mp.Vector3(sx - padding * 2,
sy - padding * 2, 0),
direction=mp.Z,
weight=-1))
nearfieldregions.append(nfrAbove)
nearfieldregions.append(nfrBelow)
return nearfieldregions
###GEOMETRY FOR THE SIMULATION#################################################
#"Material parameters"
air = mp.Medium(epsilon=1) #air dielectric value
SubstrateEps = GaN #substrate epsilon
#"Geometry to define the substrate and block of air to truncate the pyramid if self.truncation =/= 0"
geometries = []
#Substrate
geometries.append(
mp.Sphere(center=mp.Vector3(0, 0, self.distance / 2 + self.radius),
radius=self.radius,
material=CL_material))
geometries.append(
mp.Sphere(center=mp.Vector3(0, 0,
-self.distance / 2 - self.radius),
radius=self.radius,
material=CL_material))
if geometry == None:
geometries = []
if material_function == None:
material_function = None
###SYMMETRIES#########################################################
#"Symmetry logic."
if use_symmetries:
symmetry = create_symmetry(self)
print('symmetry on:', symmetry)
else:
symmetry = []
###PML_LAYERS###################################################################
pml_layer = [mp.PML(dpml)]
###SOURCE#######################################################################
#"A gaussian with pulse source proportional to exp(-iwt-(t-t_0)^2/(2w^2))"
abs_source_position_x = 0
abs_source_position_y = 0
abs_source_position_z = 0
source = [
mp.Source(
mp.GaussianSource(
frequency=self.frequency_center,
fwidth=self.frequency_width,
cutoff=self.cutoff), #gaussian current-source
component=mp.Ez,
amplitude=1,
center=mp.Vector3(abs_source_position_x, abs_source_position_y,
abs_source_position_z))
]
#source.append(mp.Source(mp.GaussianSource(frequency=self.frequency_center,fwidth=self.frequency_width, cutoff=self.cutoff), #gaussian current-source
# component=mp.Ey,
# amplitude=self.source_direction[1],
# center=mp.Vector3(abs_source_position_x,abs_source_position_y,abs_source_position_z)))
#source.append(mp.Source(mp.GaussianSource(frequency=self.frequency_center,fwidth=self.frequency_width, cutoff=self.cutoff), #gaussian current-source
# component=mp.Ez,
# amplitude=self.source_direction[2],
# center=mp.Vector3(abs_source_position_x,abs_source_position_y,abs_source_position_z)))
#MEEP simulation constructor
sim = mp.Simulation(
cell_size=cell,
geometry=geometries,
symmetries=symmetry,
sources=source,
#eps_averaging=True,
#subpixel_tol=1e-4,
#subpixel_maxeval=1000,
dimensions=3,
#default_material=GaN,
Courant=0.1,
extra_materials=[CL_material],
boundary_layers=pml_layer,
split_chunks_evenly=False,
resolution=resolution)
###SOURCE REGION###################################################
print('pixels', pixels)
def define_flux_source_regions(abs_source_position_x,
abs_source_position_y,
abs_source_position_z, resolution,
pixels):
distance = pixels * 1 / resolution
source_region = []
source_region.append(
mp.FluxRegion( #region x to calculate flux from
center=mp.Vector3(abs_source_position_x + distance,
abs_source_position_y,
abs_source_position_z),
size=mp.Vector3(0, 2 * pixels * 1 / resolution,
2 * pixels * 1 / resolution),
direction=mp.X))
source_region.append(
mp.FluxRegion( # region -x to calculate flux from
center=mp.Vector3(abs_source_position_x - distance,
abs_source_position_y,
abs_source_position_z),
size=mp.Vector3(0, 2 * pixels * 1 / resolution,
2 * pixels * 1 / resolution),
direction=mp.X,
weight=-1))
source_region.append(
mp.FluxRegion( #region y to calculate flux from
center=mp.Vector3(abs_source_position_x,
abs_source_position_y + distance,
abs_source_position_z),
size=mp.Vector3(2 * pixels * 1 / resolution, 0,
2 * pixels * 1 / resolution),
direction=mp.Y))
source_region.append(
mp.FluxRegion( #region -y to calculate flux from
center=mp.Vector3(abs_source_position_x,
abs_source_position_y - distance,
abs_source_position_z),
size=mp.Vector3(2 * pixels * 1 / resolution, 0,
2 * pixels * 1 / resolution),
direction=mp.Y,
weight=-1))
source_region.append(
mp.FluxRegion( #z-bottom region to calculate flux from
center=mp.Vector3(abs_source_position_x,
abs_source_position_y,
abs_source_position_z + distance),
size=mp.Vector3(2 * pixels * 1 / resolution,
2 * pixels * 1 / resolution, 0),
direction=mp.Z))
source_region.append(
mp.FluxRegion( #z-top region to calculate flux from
center=mp.Vector3(abs_source_position_x,
abs_source_position_y,
abs_source_position_z - distance),
size=mp.Vector3(2 * pixels * 1 / resolution,
2 * pixels * 1 / resolution, 0),
direction=mp.Z,
weight=-1))
return source_region
###REGIONS######################################################################
#"These regions define the borders of the cell with distance 'padding' between the flux region and the dpml region to avoid calculation errors."
if calculate_flux:
flux_regions = define_flux_regions(sx, sy, sz, padding)
fr1, fr2, fr3, fr4, fr5, fr6 = flux_regions
flux_total = sim.add_flux(self.frequency_center,
self.frequency_width,
self.number_of_freqs, fr1, fr2, fr3, fr4,
fr5,
fr6) #calculate flux for flux regions
if calculate_source_flux:
sr1, sr2, sr3, sr4, sr5, sr6 = define_flux_source_regions(
abs_source_position_x, abs_source_position_y,
abs_source_position_z, resolution, pixels)
flux_source = sim.add_flux(self.frequency_center,
self.frequency_width,
self.number_of_freqs, sr1, sr2, sr3,
sr4, sr5, sr6)
###FAR FIELD REGION#############################################################
#"The simulation calculates the far field flux from the regions 1-5 below. It correspons to the air above and at the side of the pyramids. The edge of the simulation cell that touches the substrate is not added to this region. Far-field calculations can not handle different materials."
if ff_calculations == True:
nearfieldregions = define_nearfield_regions(
sx, sy, sz, sh, padding, ff_cover)
if ff_cover == True:
nfrA1, nfrA2, nfrA3, nfrA4, nfrA5, nfrA6 = nearfieldregions[0]
nfrB1, nfrB2, nfrB3, nfrB4, nfrB5, nfrB6 = nearfieldregions[1]
else:
nfrA1, nfrA2, nfrA3, nfrA4, nfrA6 = nearfieldregions[0]
nfrB1, nfrB2, nfrB3, nfrB4, nfrB6 = nearfieldregions[1]
if ff_calc == "Both" and ff_cover == True:
nearfieldAbove = sim.add_near2far(self.frequency_center,
self.frequency_width,
self.number_of_freqs, nfrA1,
nfrA2, nfrA3, nfrA4, nfrA5,
nfrA6)
nearfieldBelow = sim.add_near2far(self.frequency_center,
self.frequency_width,
self.number_of_freqs, nfrB1,
nfrB2, nfrB3, nfrB4, nfrB5,
nfrB6)
elif ff_calc == "Above" and ff_cover == True:
nearfieldAbove = sim.add_near2far(self.frequency_center,
self.frequency_width,
self.number_of_freqs, nfrA1,
nfrA2, nfrA3, nfrA4, nfrA5,
nfrA6)
elif ff_calc == "Above" and ff_cover == False:
nearfieldAbove = sim.add_near2far(self.frequency_center,
self.frequency_width,
self.number_of_freqs, nfrA1,
nfrA2, nfrA3, nfrA4, nfrA6)
elif ff_calc == "Below" and ff_cover == True:
nearfieldBelow = sim.add_near2far(self.frequency_center,
self.frequency_width,
self.number_of_freqs, nfrB1,
nfrB2, nfrB3, nfrB4, nfrB5,
nfrB6)
elif ff_calc == "Below" and ff_cover == False:
nearfieldBelow = sim.add_near2far(self.frequency_center,
self.frequency_width,
self.number_of_freqs, nfrB1,
nfrB2, nfrB3, nfrB4, nfrB6)
#Assumed ff_calc == Both and ff_cover == False
else:
nearfieldAbove = sim.add_near2far(self.frequency_center,
self.frequency_width,
self.number_of_freqs, nfrA1,
nfrA2, nfrA3, nfrA4, nfrA6)
nearfieldBelow = sim.add_near2far(self.frequency_center,
self.frequency_width,
self.number_of_freqs, nfrB1,
nfrB2, nfrB3, nfrB4, nfrB6)
###RUN##########################################################################
#"Run the simulation"
if True:
sim.plot2D(output_plane=mp.Volume(
center=mp.Vector3(0, 0 * abs_source_position_y, 0),
size=mp.Vector3(0, sy + 2 * dpml, sz + 2 * dpml)))
#plt.show()
plt.savefig('foo.pdf')
sim.plot2D(output_plane=mp.Volume(
center=mp.Vector3(0 * abs_source_position_x, 0, 0),
size=mp.Vector3(sx + 2 * dpml, 0, sz + 2 * dpml)))
#plt.show()
plt.savefig('foo2.pdf')
sim.plot2D(output_plane=mp.Volume(
center=mp.Vector3(0, 0, abs_source_position_z),
size=mp.Vector3(sx + 2 * dpml, sy + 2 * dpml, 0)))
#sim.plot2D(output_plane=mp.Volume(center=mp.Vector3(0,0,sz/2-sh-0.01),size=mp.Vector3(sx+2*dpml,sy+2*dpml,0)))
plt.savefig('foo3.pdf')
if use_fixed_time:
sim.run(
mp.dft_ldos(self.frequency_center, self.frequency_width,
self.number_of_freqs),
# mp.at_beginning(mp.output_epsilon),
#until_after_sources=mp.stop_when_fields_decayed(2,mp.Ey,mp.Vector3(0,0,sbs_cource_position+0.2),1e-2))
until=simulation_time)
else:
#Withdraw maximum dipole amplitude direction
max_index = self.source_direction.index(max(self.source_direction))
if max_index == 0:
detector_pol = mp.Ex
elif max_index == 1:
detector_pol = mp.Ey
else:
detector_pol = mp.Ez
#TODO: exchange self.source_direction to maxmimum dipole ampltitude
sim.run(
mp.dft_ldos(self.frequency_center, self.frequency_width,
self.number_of_freqs),
#mp.to_appended("ex", mp.at_every(0.6, mp.output_efield_x)),
mp.at_beginning(mp.output_epsilon),
until_after_sources=mp.stop_when_fields_decayed(
2, detector_pol,
mp.Vector3(0, 0, abs_source_position_z + 0.2), 1e-3))
###OUTPUT CALCULATIONS##########################################################
#"Calculate the poynting flux given the far field values of E, H."
myIntegration = True
nfreq = self.number_of_freqs
r = 2 * math.pow(
self.pyramid_height, 2
) * self.frequency_center * 2 * 10 # 10 times the Fraunhofer-distance
if ff_calculations:
fields = []
P_tot_ff = np.zeros(self.number_of_freqs)
npts = ff_pts #number of far-field points
Px = 0
Py = 0
Pz = 0
theta = ff_angle
phi = math.pi * 2
#"How many points on the ff-sphere"
#global xPts
#xPts=[]
#global yPts
#yPts=[]
#global zPts
#zPts=[]
Pr_Array = []
if myIntegration == True:
#how to pick ff-points, this uses fibbonaci-sphere distribution
if FibonacciSampling == True:
if theta == math.pi / 3:
offset = 1.5 / npts
elif theta == math.pi / 4:
npts = npts * 2
offset = 1.15 / npts
elif theta == math.pi / 5:
npts = npts * 2.5
offset = 0.95 / npts
elif theta == math.pi / 6:
#npts=npts*3
offset = 0.8 / npts
elif theta == math.pi / 7:
npts = npts * 3
offset = 0.7 / npts
elif theta == math.pi / 8:
npts = npts * 3
offset = 0.6 / npts
elif theta == math.pi / 12:
npts = npts * 3
offset = 0.4 / npts
else:
offset = 0.2 / npts
xPts, yPts, zPts = fibspherepts(r, theta, npts, offset)
range_npts = int((theta / math.pi) * npts)
else:
#check out Lebedev quadrature
#if not fibb sampling then spherical sampling
theta_pts = npts
phi_pts = npts * 2
xPts, yPts, zPts = sphericalpts(r, theta, phi, theta_pts,
phi_pts)
range_npts = int(theta_pts * phi_pts + 1)
if ff_calc == "Both":
#Pr_ArrayA for above, B for below
Pr_ArrayA = []
Pr_ArrayB = []
P_tot_ffA = [0] * (self.number_of_freqs)
P_tot_ffB = [0] * (self.number_of_freqs)
for n in range(range_npts):
ffA = sim.get_farfield(
nearfieldAbove,
mp.Vector3(xPts[n], yPts[n], zPts[n]))
ffB = sim.get_farfield(
nearfieldBelow,
mp.Vector3(xPts[n], yPts[n], -1 * zPts[n]))
i = 0
for k in range(nfreq):
"Calculate the poynting vector in x,y,z direction"
PrA = myPoyntingFlux(ffA, i)
PrB = myPoyntingFlux(ffB, i)
Pr_ArrayA.append(PrA)
Pr_ArrayB.append(PrB)
"the spherical cap has area 2*pi*r^2*(1-cos(theta))"
"divided by npts and we get evenly sized area chunks"
surface_Element = 2 * math.pi * pow(
r, 2) * (1 - math.cos(theta)) / range_npts
P_tot_ffA[k] += surface_Element * (1) * (PrA)
P_tot_ffB[k] += surface_Element * (1) * (PrB)
i = i + 6 #to keep track of the correct entries in the ff array
if ff_calc == "Below":
for n in range(range_npts):
ff = sim.get_farfield(
nearfieldBelow,
mp.Vector3(xPts[n], yPts[n], -1 * zPts[n]))
fields.append({
"pos": (xPts[n], yPts[n], zPts[n]),
"field": ff
})
i = 0
for k in range(nfreq):
"Calculate the poynting vector in x,y,z direction"
Pr = myPoyntingFlux(ff, i)
Pr_Array.append(Pr)
"the spherical cap has area 2*pi*r^2*(1-cos(theta))"
"divided by npts and we get evenly sized area chunks"
surface_Element = 2 * math.pi * pow(
r, 2) * (1 - math.cos(theta)) / range_npts
P_tot_ff[k] += surface_Element * (1) * (Pr)
i = i + 6 #to keep track of the correct entries in the ff array
if ff_calc == "Above":
for n in range(range_npts):
ff = sim.get_farfield(
nearfieldAbove,
mp.Vector3(xPts[n], yPts[n], zPts[n]))
fields.append({
"pos": (xPts[n], yPts[n], zPts[n]),
"field": ff
})
# print('ff,n,x,y,z',n,xPts[n],yPts[n],zPts[n],ff)
# print('fields',fields[n])
# print('------')
i = 0
for k in range(nfreq):
"Calculate the poynting vector in x,y,z direction"
Pr = myPoyntingFlux(ff, i)
Pr_Array.append(Pr)
"the spherical cap has area 2*pi*r^2*(1-cos(theta))"
"divided by npts and we get evenly sized area chunks"
surface_Element = 2 * math.pi * pow(
r, 2) * (1 - math.cos(theta)) / range_npts
P_tot_ff[k] += surface_Element * (1) * (Pr)
#print('S',surface_Element,'r',r,'theta',theta,'range npts',range_npts)
i = i + 6 #to keep track of the correct entries in the ff array
# print('P_tot_ff',P_tot_ff)
# print('fields',fields)
# print('Pr_Array',Pr_Array)
##CALCULATE FLUX OUT FROM BOX###########################################
if calculate_flux:
#"Initialize variables to be used, pf stands for 'per frequency'"
flux_tot_value = np.zeros(
self.number_of_freqs) #total flux out from box
flux_tot_ff_ratio = np.zeros(self.number_of_freqs)
flux_tot_out = mp.get_fluxes(flux_total) #save total flux data
freqs_out = mp.get_flux_freqs(flux_total)
print('freqs', freqs_out)
if calculate_source_flux:
source_flux_out = mp.get_fluxes(flux_source)
elapsed_time = round((time.time() - start) / 60, 1)
print('LDOS', sim.ldos_data)
print('LDOS0', sim.ldos_data[0])
for i in range(len(flux_tot_out)):
print(flux_tot_out[i] * 100 / source_flux_out[i],
'LE percentage for lambda: ', 1 / freqs_out[i])
if False:
fig = plt.figure()
ax = fig.gca(projection='3d')
Pr_Max = max(Pr_Array)
R = [n / Pr_Max for n in Pr_Array]
print(R)
# R=1
pts = len(Pr_Array)
theta, phi = np.linspace(0, np.pi,
pts), np.linspace(0, 2 * np.pi, pts)
THETA, PHI = np.meshgrid(theta, phi)
#print(xPts)
# print(yPts)
# print(zPts)
X = np.zeros(pts**2)
Y = np.zeros(pts**2)
Z = np.zeros(pts**2)
print('R pts', pts)
print('sample pts', len(xPts))
for n in range(pts):
xPts[n] = R[n] * xPts[n]
yPts[n] = R[n] * yPts[n]
zPts[n] = R[n] * zPts[n]
# #print(X)
# #print(Y)
# #print(Z)
#ax.set_xlim(-100,100)
#ax.set_zlim(-100,100)
#ax.set_ylim(-100,100)
#ax.scatter(xPts,yPts,zPts)
u = np.linspace(0, 2 * np.pi, 120)
v = np.linspace(0, np.pi / 6, 120)
r_ = np.asarray(R)
x = np.outer(np.cos(u), np.sin(v))
y = np.outer(np.sin(u), np.sin(v))
z = R * np.outer(np.ones(np.size(u)), np.cos(v))
print('lenx', len(x), 'leny', len(y), 'lenz', len(z))
#r = np.sqrt(xPts**2+yPts**2+zPts**2)
#plot(r)
ax.plot_surface(x, y, z, cmap='plasma')
#ax.quiver(0,0,0,0,0,1,length=1.2,color='brown',normalize='true')
#ax.text(0,0,1.3, '$\mathcal{P}$',size=20, zdir=None)
#ax.set_zlim(-1,1)
#ax.axis('off')
#ax.plot_trisurf(list(x),list(y),list(z),cmap='plasma')
plt.show()
for n in range(len(flux_tot_out)):
flux_tot_out[n] = round(flux_tot_out[n], 11)
# P_tot_ff[n]=round(P_tot_ff[n],9)
##Some processing to calculate the flux ratios per frequency
if ff_calculations:
for n in range(len(flux_tot_out)):
# flux_tot_out[n]=round(flux_tot_out[n],9)
P_tot_ff[n] = round(P_tot_ff[n], 11)
for i in range(self.number_of_freqs):
flux_tot_ff_ratio[i] = round(P_tot_ff[i] / flux_tot_out[i],
11)
if ff_calc == "Both":
P_tot_ff = []
P_tot_ff.append(P_tot_ffA)
P_tot_ff.append(P_tot_ffB)
flux_tot_ff_ratio = []
flux_tot_ff_ratioA = [0] * (self.number_of_freqs)
flux_tot_ff_ratioB = [0] * (self.number_of_freqs)
for i in range(self.number_of_freqs):
flux_tot_ff_ratioA[i] = round(
P_tot_ffA[i] / flux_tot_out[i], 11)
flux_tot_ff_ratioB[i] = round(
P_tot_ffB[i] / flux_tot_out[i], 11)
flux_tot_ff_ratio.append(flux_tot_ff_ratioA)
flux_tot_ff_ratio.append(flux_tot_ff_ratioB)
return {
"total_flux": flux_tot_out,
"source_flux": source_flux_out,
"ff_at_angle": P_tot_ff,
"flux_ratio": flux_tot_ff_ratio,
"LDOS": sim.ldos_data,
"Elapsed time (min)": elapsed_time
}
else:
return {
"total_flux": flux_tot_out,
"source_flux": source_flux_out,
"ff_at_angle": None,
"flux_ratio": None,
"LDOS": sim.ldos_data,
"Elapsed time (min)": elapsed_time
}
mp.Vector3(0, 0.5, 0.5), # X
mp.Vector3(0.25, 0.75, 0.5), # W
mp.Vector3(0.375, 0.75, 0.375) # K
]
k_points = mp.interpolate(4, vlist)
# define a couple of parameters (which we can set from the command_line)
eps = 11.56 # the dielectric constant of the spheres
r = 0.25 # the radius of the spheres
diel = mp.Medium(epsilon=eps)
# A diamond lattice has two "atoms" per unit cell:
geometry = [
mp.Sphere(r, center=mp.Vector3(0.125, 0.125, 0.125), material=diel),
mp.Sphere(r, center=mp.Vector3(-0.125, -0.125, -0.125), material=diel)
]
# (A simple fcc lattice would have only one sphere/object at the origin.)
resolution = 16 # use a 16x16x16 grid
mesh_size = 5
num_bands = 5
ms = mpb.ModeSolver(geometry_lattice=geometry_lattice,
k_points=k_points,
geometry=geometry,
resolution=resolution,
num_bands=num_bands,
mesh_size=mesh_size)
def main(series, folder, resolution, from_um_factor, r, paper, wlen):
#%% PARAMETERS
# Au sphere
r = r / (from_um_factor * 1e3) # Radius of sphere now in Meep units
medium = import_medium("Au", from_um_factor,
paper=paper) # Medium of sphere: gold (Au)
# Frequency and wavelength
wlen = wlen / (from_um_factor * 1e3) # Wavelength now in Meep units
# Space configuration
pml_width = 0.38 * wlen # 0.5 * wlen
air_width = r / 2 # 2 * r
# Field Measurements
period_line = 1
period_plane = 1
after_cell_run_time = 10 * wlen
# Computation time
enlapsed = []
# Saving directories
if series is None:
series = f"AuSphereField{2*r*from_um_factor*1e3:.0f}WLen{wlen*from_um_factor*1e3:.0f}"
if folder is None:
folder = "AuMieSphere/AuSphereField"
home = vs.get_home()
#%% GENERAL GEOMETRY SETUP
air_width = air_width - air_width % (1 / resolution)
pml_width = pml_width - pml_width % (1 / resolution)
pml_layers = [mp.PML(thickness=pml_width)]
symmetries = [mp.Mirror(mp.Y), mp.Mirror(mp.Z, phase=-1)]
# Cause of symmetry, two mirror planes reduce cell size to 1/4
cell_width = 2 * (pml_width + air_width + r)
cell_width = cell_width - cell_width % (1 / resolution)
cell_size = mp.Vector3(cell_width, cell_width, cell_width)
source_center = -0.5 * cell_width + pml_width
print("Resto Source Center: {}".format(source_center % (1 / resolution)))
sources = [
mp.Source(mp.ContinuousSource(wavelength=wlen, is_integrated=True),
center=mp.Vector3(source_center),
size=mp.Vector3(0, cell_width, cell_width),
component=mp.Ez)
]
# Ez-polarized monochromatic planewave
# (its size parameter fills the entire cell in 2d)
# >> The planewave source extends into the PML
# ==> is_integrated=True must be specified
geometry = [mp.Sphere(material=medium, center=mp.Vector3(), radius=r)]
# Au sphere with frequency-dependant characteristics imported from Meep.
path = os.path.join(home, folder, series)
if not os.path.isdir(path): vs.new_dir(path)
file = lambda f: os.path.join(path, f)
#%% SAVE GET FUNCTIONS
def get_line(sim):
return sim.get_array(center=mp.Vector3(),
size=mp.Vector3(cell_width),
component=mp.Ez)
def get_plane(sim):
return sim.get_array(center=mp.Vector3(),
size=mp.Vector3(0, cell_width, cell_width),
component=mp.Ez)
#%% INITIALIZE
sim = mp.Simulation(resolution=resolution,
cell_size=cell_size,
boundary_layers=pml_layers,
sources=sources,
symmetries=symmetries,
geometry=geometry)
temp = time()
sim.init_sim()
enlapsed.append(time() - temp)
#%% DEFINE SAVE STEP FUNCTIONS
f, save_line = vs.save_slice_generator(sim, file("Lines.h5"), "Ez",
get_line)
g, save_plane = vs.save_slice_generator(sim, file("Planes.h5"), "Ez",
get_plane)
to_do_while_running = [
mp.at_every(period_line, save_line),
mp.at_every(period_plane, save_plane)
]
#%% RUN!
temp = time()
sim.run(*to_do_while_running, until=cell_width + after_cell_run_time)
del f, g
enlapsed.append(time() - temp)
#%% SAVE METADATA
params = dict(from_um_factor=from_um_factor,
resolution=resolution,
r=r,
paper=paper,
pml_width=pml_width,
air_width=air_width,
cell_width=cell_width,
source_center=source_center,
wlen=wlen,
period_line=period_line,
period_plane=period_plane,
after_cell_run_time=after_cell_run_time,
series=series,
folder=folder,
home=home,
enlapsed=enlapsed)
f = h5.File(file("Lines.h5"), "r+")
for a in params:
f["Ez"].attrs[a] = params[a]
f.close()
del f
g = h5.File(file("Planes.h5"), "r+")
for a in params:
g["Ez"].attrs[a] = params[a]
g.close()
del g
sim.reset_meep()
def __init__(self, dir_name, wavelength, thy_absorb, cyt_absorb):
self.base_directory = base_directory + str(dir_name)
self.wavelength = wavelength
self.thy_absorb = thy_absorb
self.cyt_absorb = cyt_absorb
self.frequency = 1 / wavelength
# Calculate wavelengths dependent on RI
self.wavelength_in_media = wavelength / ri_media
self.wavelength_in_cytoplasm = wavelength / ri_cytoplasm
self.wavelength_in_thylakoid = wavelength / ri_thylakoid
max_freq = self.frequency - 0.01
min_freq = self.frequency + 0.01
self.pulse_width = abs(max_freq - min_freq)
cell = mp.Vector3(sxx, sxy, sxz)
pml_layers = [mp.PML(dpml)]
thylakoid_material = mp.Medium(index=ri_thylakoid,
D_conductivity=2 * math.pi *
self.frequency * (thy_absorb /
(ri_thylakoid**2)))
cytoplasm_material = mp.Medium(index=ri_cytoplasm,
D_conductivity=2 * math.pi *
self.frequency * (cyt_absorb /
(ri_cytoplasm**2)))
thylakoid_region = mp.Sphere(radius=cell_radius,
center=mp.Vector3(0, 0, 0),
material=thylakoid_material)
cytoplasm_region = mp.Sphere(radius=cell_radius - thylakoid_thickness,
center=mp.Vector3(0, 0, 0),
material=cytoplasm_material)
geometry = [thylakoid_region, cytoplasm_region]
# Sources
kdir = mp.Vector3(1, 0, 0) # direction of k (length is irrelevant)
n = ri_media # refractive index of material containing the source
k = kdir.unit().scale(2 * math.pi * self.frequency *
n) # k with correct length
def pw_amp(k, x0):
def _pw_amp(x):
return cmath.exp(1j * k.dot(x + x0))
return _pw_amp
source = [
mp.Source(
mp.ContinuousSource(frequency=self.frequency,
fwidth=self.pulse_width), # along x axis
component=mp.Ez,
center=mp.Vector3(-0.5 * simulation_size, 0, 0), # x, ,y ,z
size=mp.Vector3(0, sxy, sxz),
amp_func=pw_amp(k, mp.Vector3(x=-0.5 * simulation_size)))
]
sim = mp.Simulation(
cell_size=cell,
sources=source,
boundary_layers=pml_layers,
resolution=resolution,
geometry=geometry,
default_material=mp.Medium(index=ri_media),
force_complex_fields=complex_f,
eps_averaging=eps_av,
)
def output_fields(sim):
ez_output = open(base_directory + "Ez Field 430 NoAbs" + ".npy",
'wb')
ez_array = sim.get_array(component=mp.Ez, cmplx=complex_f)
ez_field_output = np.asarray(ez_array)
np.save(ez_output, ez_field_output)
ez_output.close()
# ey_output = open(base_directory + "Ey Field 300 Std" + ".npy", 'wb')
# ey_array = sim.get_array(component=mp.Ey, cmplx=complex_f)
# ey_field_output = np.asarray(ey_array)
# np.save(ey_output, ey_field_output)
# ey_output.close()
#
# ex_output = open(base_directory + "Ex Field 300 std abs" + ".npy", 'wb')
# ex_array = sim.get_array(component=mp.Ex, cmplx=complex_f)
# ex_field_output = np.asarray(ex_array)
# np.save(ex_output, ex_field_output)
# ex_output.close()
# eps_output = open(base_directory + "Refractive Index" + ".npy", 'wb')
# eps_array = sim.get_array(component=mp.Dielectric, cmplx=complex_f)
# np.save(eps_output, eps_array)
# eps_output.close()
sim.use_output_directory(self.base_directory)
sim.run(mp.at_every(1, output_fields), until=t)
def main(args):
resolution = 30
nSiO2 = 1.4
SiO2 = mp.Medium(index=nSiO2)
# conversion factor for eV to 1/um
eV_um_scale = 1 / 1.23984193
# W, from Rakic et al., Applied Optics, vol. 32, p. 5274 (1998)
W_eps_inf = 1
W_plasma_frq = 13.22 * eV_um_scale
W_f0 = 0.206
W_frq0 = 1e-10
W_gam0 = 0.064 * eV_um_scale
W_sig0 = W_f0 * W_plasma_frq**2 / W_frq0**2
W_f1 = 0.054
W_frq1 = 1.004 * eV_um_scale # 1.235 um
W_gam1 = 0.530 * eV_um_scale
W_sig1 = W_f1 * W_plasma_frq**2 / W_frq1**2
W_f2 = 0.166
W_frq2 = 1.917 * eV_um_scale # 0.647
W_gam2 = 1.281 * eV_um_scale
W_sig2 = W_f2 * W_plasma_frq**2 / W_frq2**2
W_susc = [
mp.DrudeSusceptibility(frequency=W_frq0, gamma=W_gam0, sigma=W_sig0),
mp.LorentzianSusceptibility(frequency=W_frq1,
gamma=W_gam1,
sigma=W_sig1),
mp.LorentzianSusceptibility(frequency=W_frq2,
gamma=W_gam2,
sigma=W_sig2)
]
W = mp.Medium(epsilon=W_eps_inf, E_susceptibilities=W_susc)
# crystalline Si, from M.A. Green, Solar Energy Materials and Solar Cells, vol. 92, pp. 1305-1310 (2008)
# fitted Lorentzian parameters, only for 600nm-1100nm
Si_eps_inf = 9.14
Si_eps_imag = -0.0334
Si_eps_imag_frq = 1 / 1.55
Si_frq = 2.2384
Si_gam = 4.3645e-02
Si_sig = 14.797 / Si_frq**2
Si = mp.Medium(epsilon=Si_eps_inf,
D_conductivity=2 * math.pi * Si_eps_imag_frq * Si_eps_imag /
Si_eps_inf,
E_susceptibilities=[
mp.LorentzianSusceptibility(frequency=Si_frq,
gamma=Si_gam,
sigma=Si_sig)
])
a = args.a # lattice periodicity
cone_r = args.cone_r # cone radius
cone_h = args.cone_h # cone height
wire_w = args.wire_w # metal-grid wire width
wire_h = args.wire_h # metal-grid wire height
trench_w = args.trench_w # trench width
trench_h = args.trench_h # trench height
Np = args.Np # number of periods in supercell
dair = 1.0 # air gap thickness
dmcl = 1.7 # micro lens thickness
dsub = 3000.0 # substrate thickness
dpml = 1.0 # PML thickness
sxy = Np * a
sz = dpml + dair + dmcl + dsub + dpml
cell_size = mp.Vector3(sxy, sxy, sz)
boundary_layers = [
mp.PML(dpml, direction=mp.Z, side=mp.High),
mp.Absorber(dpml, direction=mp.Z, side=mp.Low)
]
geometry = []
if args.substrate:
geometry = [
mp.Sphere(material=SiO2,
radius=dmcl,
center=mp.Vector3(0, 0, 0.5 * sz - dpml - dair - dmcl)),
mp.Block(material=Si,
size=mp.Vector3(mp.inf, mp.inf, dsub + dpml),
center=mp.Vector3(0, 0, -0.5 * sz + 0.5 * (dsub + dpml))),
mp.Block(
material=W,
size=mp.Vector3(mp.inf, wire_w, wire_h),
center=mp.Vector3(0, -0.5 * sxy + 0.5 * wire_w,
-0.5 * sz + dpml + dsub + 0.5 * wire_h)),
mp.Block(
material=W,
size=mp.Vector3(mp.inf, wire_w, wire_h),
center=mp.Vector3(0, +0.5 * sxy - 0.5 * wire_w,
-0.5 * sz + dpml + dsub + 0.5 * wire_h)),
mp.Block(
material=W,
size=mp.Vector3(wire_w, mp.inf, wire_h),
center=mp.Vector3(-0.5 * sxy + 0.5 * wire_w, 0,
-0.5 * sz + dpml + dsub + 0.5 * wire_h)),
mp.Block(material=W,
size=mp.Vector3(wire_w, mp.inf, wire_h),
center=mp.Vector3(+0.5 * sxy - 0.5 * wire_w, 0,
-0.5 * sz + dpml + dsub + 0.5 * wire_h))
]
if args.substrate and args.texture:
for nx in range(Np):
for ny in range(Np):
cx = -0.5 * sxy + (nx + 0.5) * a
cy = -0.5 * sxy + (ny + 0.5) * a
geometry.append(
mp.Cone(material=SiO2,
radius=0,
radius2=cone_r,
height=cone_h,
center=mp.Vector3(
cx, cy,
0.5 * sz - dpml - dair - dmcl - 0.5 * cone_h)))
if args.substrate:
geometry.append(
mp.Block(material=SiO2,
size=mp.Vector3(mp.inf, trench_w, trench_h),
center=mp.Vector3(
0, -0.5 * sxy + 0.5 * trench_w,
0.5 * sz - dpml - dair - dmcl - 0.5 * trench_h)))
geometry.append(
mp.Block(material=SiO2,
size=mp.Vector3(mp.inf, trench_w, trench_h),
center=mp.Vector3(
0, +0.5 * sxy - 0.5 * trench_w,
0.5 * sz - dpml - dair - dmcl - 0.5 * trench_h)))
geometry.append(
mp.Block(material=SiO2,
size=mp.Vector3(trench_w, mp.inf, trench_h),
center=mp.Vector3(
-0.5 * sxy + 0.5 * trench_w, 0,
0.5 * sz - dpml - dair - dmcl - 0.5 * trench_h)))
geometry.append(
mp.Block(material=SiO2,
size=mp.Vector3(trench_w, mp.inf, trench_h),
center=mp.Vector3(
+0.5 * sxy - 0.5 * trench_w, 0,
0.5 * sz - dpml - dair - dmcl - 0.5 * trench_h)))
k_point = mp.Vector3(0, 0, 0)
lambda_min = 0.7 # minimum source wavelength
lambda_max = 1.0 # maximum source wavelength
fmin = 1 / lambda_max
fmax = 1 / lambda_min
fcen = 0.5 * (fmin + fmax)
df = fmax - fmin
sources = [
mp.Source(mp.GaussianSource(fcen, fwidth=df),
component=mp.Ex,
center=mp.Vector3(0, 0, 0.5 * sz - dpml - 0.5 * dair),
size=mp.Vector3(sxy, sxy, 0))
]
sim = mp.Simulation(resolution=resolution,
cell_size=cell_size,
boundary_layers=boundary_layers,
geometry=geometry,
dimensions=3,
k_point=k_point,
sources=sources)
nfreq = 50
refl = sim.add_flux(
fcen, df, nfreq,
mp.FluxRegion(center=mp.Vector3(0, 0, 0.5 * sz - dpml),
size=mp.Vector3(sxy, sxy, 0)))
trans_grid = sim.add_flux(
fcen, df, nfreq,
mp.FluxRegion(center=mp.Vector3(0, 0,
-0.5 * sz + dpml + dsub + wire_h),
size=mp.Vector3(sxy, sxy, 0)))
trans_sub_top = sim.add_flux(
fcen, df, nfreq,
mp.FluxRegion(center=mp.Vector3(0, 0, -0.5 * sz + dpml + dsub),
size=mp.Vector3(sxy, sxy, 0)))
trans_sub_bot = sim.add_flux(
fcen, df, nfreq,
mp.FluxRegion(center=mp.Vector3(0, 0, -0.5 * sz + dpml),
size=mp.Vector3(sxy, sxy, 0)))
sim.run(mp.at_beginning(mp.output_epsilon), until=0)
if args.substrate:
sim.load_minus_flux('refl-flux', refl)
sim.run(until_after_sources=mp.stop_when_fields_decayed(
50, mp.Ex, mp.Vector3(0, 0, -0.5 * sz + dpml + 0.5 * dsub), 1e-9))
if not args.substrate:
sim.save_flux('refl-flux', refl)
sim.display_fluxes(refl, trans_grid, trans_sub_top, trans_sub_bot)
import pinboard
job = pinboard.pinboard()
nm = 1e-9
um = 1e-6
### geometry
radius = 75 * nm
gold = meep_ext.material.Au()
gold = meep.Medium(index=3.5)
sep = 400 * nm
p1 = meep.Vector3(-sep / 2, 0, 0)
p2 = meep.Vector3(sep / 2, 0, 0)
geometry = [
meep.Sphere(center=p1, radius=radius, material=gold),
meep.Sphere(center=p2, radius=radius, material=gold)
]
### source
fcen, df = meep_ext.freq_data(1 / (400 * nm), 1 / (1000 * nm))
nfreq = 40
src_time = meep.GaussianSource(frequency=1.3 / um, fwidth=4.0 / um)
polarization = meep.Ex # used in convergence check 'decay_by'
source = lambda sim: meep_ext.x_polarized_plane_wave(sim, src_time)
### monitor info
particle_monitor_gap = 50 * nm
pml_monitor_gap = 50 * nm
norm_file_ext = 'norm'
monitor_size = [
def run_simulation(save_prefix,
tip_radius=0.007,
cone_height=0.364,
trunk_radius=0.275,
n_tip=3.694,
k_tip=0.0,
fcen=1.25,
waves=7.5,
theta_deg=10,
sample=20,
sx=0.8,
sy=1.5,
sz=1.0,
dpml=0.1,
res=1000,
res_factor=0.2,
X_1=-0.2,
X_2=0.2,
Y_1=-0.2,
Y_2=0.2,
Z_1=-0.2,
Z_2=0.2,
x_mon_rat=1.0,
y_mon_rat=1.0,
z_mon_rat=1.0):
#Interpolate to next resolution step for high-res region
dx = 1 / res
X_1 = np.floor(X_1 / dx) * dx
X_2 = np.ceil(X_2 / dx) * dx
Y_1 = np.floor(Y_1 / dx) * dx
Y_2 = np.ceil(Y_2 / dx) * dx
Z_1 = np.floor(Z_1 / dx) * dx
Z_2 = np.ceil(Z_2 / dx) * dx
#Dump all the settings to a file:
settings_file = h5py.File(
Path(sys.argv[0]).stem + '-' + save_prefix + '_settings.h5', 'w')
settings_file.create_dataset('tip_radius', data=tip_radius)
settings_file.create_dataset('cone_height', data=cone_height)
settings_file.create_dataset('trunk_radius', data=trunk_radius)
settings_file.create_dataset('n_tip', data=n_tip)
settings_file.create_dataset('k_tip', data=k_tip)
settings_file.create_dataset('fcen', data=fcen)
settings_file.create_dataset('waves', data=waves)
settings_file.create_dataset('theta_deg', data=theta_deg)
settings_file.create_dataset('sample', data=sample)
settings_file.create_dataset('sx', data=sx)
settings_file.create_dataset('sy', data=sy)
settings_file.create_dataset('sz', data=sz)
settings_file.create_dataset('dpml', data=dpml)
settings_file.create_dataset('res', data=res)
settings_file.create_dataset('res_factor', data=res_factor)
settings_file.create_dataset('X_1', data=X_1)
settings_file.create_dataset('X_2', data=X_2)
settings_file.create_dataset('Y_1', data=Y_1)
settings_file.create_dataset('Y_2', data=Y_2)
settings_file.create_dataset('Z_1', data=Z_1)
settings_file.create_dataset('Z_2', data=Z_2)
settings_file.create_dataset('x_mon_rat', data=x_mon_rat)
settings_file.create_dataset('y_mon_rat', data=y_mon_rat)
settings_file.create_dataset('z_mon_rat', data=z_mon_rat)
settings_file.close()
#Convert theta to radians
theta = theta_deg * np.pi / 180
eps_tip = calc_eps_r(n_tip, k_tip)
sig_d_tip = calc_sig_d(n_tip, k_tip, fcen)
#Create the cell size
sX = 2 * dpml + sx
sY = 2 * dpml + sy
sZ = 2 * dpml + sz
#Monitor sizes
x_mon = sx * x_mon_rat
y_mon = sx * y_mon_rat
z_mon = sx * z_mon_rat
#Calculate values in prime-space:
sx_prime = sx * res_factor + (X_2 - X_1) * (1 - res_factor)
sy_prime = sy * res_factor + (Y_2 - Y_1) * (1 - res_factor)
sz_prime = sz * res_factor + (Z_2 - Z_1) * (1 - res_factor)
dpml_prime = dpml * res_factor
sX_prime = 2 * dpml_prime + sx_prime
sY_prime = 2 * dpml_prime + sy_prime
sZ_prime = 2 * dpml_prime + sz_prime
x_mon_prime = (x_mon/2.0 > X_2)*((x_mon/2.0 - X_2)*res_factor + X_2) +\
(x_mon/2.0)*(x_mon/2.0 <= X_2) -\
(-1*x_mon/2.0 < X_1)*((-1*x_mon/2.0 - X_1)*res_factor + X_1) -\
(-1*x_mon/2.0)*(-1*x_mon/2.0 >= X_1)
y_mon_prime = (y_mon/2.0 > Y_2)*((y_mon/2.0 - Y_2)*res_factor + Y_2) +\
(y_mon/2.0)*(y_mon/2.0 <= Y_2) -\
(-1*y_mon/2.0 < Y_1)*((-1*y_mon/2.0 - Y_1)*res_factor + Y_1) -\
(-1*y_mon/2.0)*(-1*y_mon/2.0 >= Y_1)
z_mon_prime = (z_mon/2.0 > Z_2)*((z_mon/2.0 - Z_2)*res_factor + Z_2) +\
(z_mon/2.0)*(z_mon/2.0 <= Z_2) -\
(-1*z_mon/2.0 < Z_1)*((-1*z_mon/2.0 - Z_1)*res_factor + Z_1) -\
(-1*z_mon/2.0)*(-1*z_mon/2.0 >= Z_1)
cell = mp.Vector3(sX_prime, sY_prime, sZ_prime)
tip = [
mp.Cylinder(radius=trunk_radius,
center=mp.Vector3(
0.0, -1 * sY / 4.0 - cone_height / 2.0 - tip_radius,
0.0),
height=(sY / 2.0 - cone_height),
axis=mp.Vector3(0.0, 1.0, 0.0)),
mp.Cone(center=mp.Vector3(0, -1 * cone_height / 2 - tip_radius, 0),
height=cone_height,
radius=trunk_radius,
radius2=tip_radius,
axis=mp.Vector3(0, 1, 0)),
mp.Sphere(center=mp.Vector3(0, -1 * tip_radius, 0), radius=tip_radius)
]
def mat_func(r_prime):
r_x = r_prime.x
r_y = r_prime.y
r_z = r_prime.z
x_fac = 1
y_fac = 1
z_fac = 1
if (r_prime.x < X_1):
x_fac = res_factor
r_x = X_1 + (r_prime.x - X_1) / res_factor
elif (r_prime.x > X_2):
x_fac = res_factor
r_x = X_2 + (r_prime.x - X_2) / res_factor
if (r_prime.y < Y_1):
y_fac = res_factor
r_y = Y_1 + (r_prime.y - Y_1) / res_factor
elif (r_prime.y > Y_2):
y_fac = res_factor
r_y = Y_2 + (r_prime.y - Y_2) / res_factor
if (r_prime.z < Z_1):
z_fac = res_factor
r_z = Z_1 + (r_prime.z - Z_1) / res_factor
elif (r_prime.z > Z_2):
z_fac = res_factor
r_z = Z_2 + (r_prime.z - Z_2) / res_factor
r = mp.Vector3(r_x, r_y, r_z)
J = np.matrix([[x_fac, 0, 0], [0, y_fac, 0], [0, 0, z_fac]])
#Loop through all objects inside of tip and see if point is inside.
# if yes -- then set eps_point to tip eps
# if no -- then leave it as air
eps_point = 1.0
for kk in range(len(tip)):
if (mp.is_point_in_object(r, tip[kk])):
eps_point = eps_tip
eps_transform = eps_point * J * J.transpose() / np.linalg.det(J)
mu_transform = J * J.transpose() / np.linalg.det(J)
eps_diag = eps_transform.diagonal()
mu_diag = mu_transform.diagonal()
mat = mp.Medium(epsilon_diag=mp.Vector3(eps_diag[0, 0], eps_diag[0, 1],
eps_diag[0, 2]),
mu_diag=mp.Vector3(mu_diag[0, 0], mu_diag[0, 1],
mu_diag[0, 2]),
D_conductivity=sig_d_tip)
return mat
#Create source amplitude function:
ky = fcen * np.sin(theta)
ky_prime = ky * sY / sY_prime
def my_amp_func_y(r_prime):
r_y = r_prime.y
y_fac = 1 / res_factor
if ((r_prime.x >= X_1) and (r_prime.x <= X_2)):
x_fac = 1.0 / res_factor
else:
x_fac = 1.0
if (r_prime.y < Y_1):
y_fac = 1.0
r_y = Y_1 + (r_prime.y - Y_1) / res_factor
elif (r_prime.y > Y_2):
y_fac = 1.0
r_y = Y_2 + (r_prime.y - Y_2) / res_factor
if ((r_prime.z >= Z_1) and (r_prime.z <= Z_2)):
z_fac = 1.0 / res_factor
else:
z_fac = 1.0
J = np.matrix([[x_fac, 0, 0], [0, y_fac, 0], [0, 0, z_fac]])
transform = J / np.linalg.det(J)
phase_factor = np.exp(-1 * 2 * 1j * np.pi * ky * r_y)
amp_factor = transform.diagonal()[0, 1]
return amp_factor * phase_factor
def my_amp_func_z(r_prime):
r_y = r_prime.y
y_fac = 1.0 / res_factor
if ((r_prime.x >= X_1) and (r_prime.x <= X_2)):
x_fac = 1.0 / res_factor
else:
x_fac = 1.0
if (r_prime.y < Y_1):
y_fac = 1.0
r_y = Y_1 + (r_prime.y - Y_1) / res_factor
elif (r_prime.y > Y_2):
y_fac = 1.0
r_y = Y_2 + (r_prime.y - Y_2) / res_factor
if ((r_prime.z >= Z_1) and (r_prime.z <= Z_2)):
z_fac = 1.0 / res_factor
else:
z_fac = 1.0
J = np.matrix([[x_fac, 0, 0], [0, y_fac, 0], [0, 0, z_fac]])
transform = J / np.linalg.det(J)
phase_factor = np.exp(-1 * 2 * 1j * np.pi * ky * r_y)
amp_factor = transform.diagonal()[0, 2]
return amp_factor * phase_factor
#Create PMLs
pml_layers = [
mp.PML(thickness=dpml_prime, direction=mp.X),
mp.PML(thickness=dpml_prime, direction=mp.Y),
mp.PML(thickness=dpml_prime, direction=mp.Z)
]
symmetry = [mp.Mirror(direction=mp.X)]
#Sources
Ey_source = mp.Source(mp.ContinuousSource(frequency=fcen),
component=mp.Ey,
center=mp.Vector3(0, 0, -1 * sz_prime * 0.5),
size=mp.Vector3(sX_prime, sY_prime, 0),
amp_func=my_amp_func_y,
amplitude=np.cos(theta))
Ez_source = mp.Source(mp.ContinuousSource(frequency=fcen),
component=mp.Ez,
center=mp.Vector3(0, 0, -1 * sz_prime * 0.5),
size=mp.Vector3(sX_prime, sY_prime, 0),
amp_func=my_amp_func_z,
amplitude=np.sin(theta))
sources = [Ey_source, Ez_source]
monitor_xy = mp.Volume(center=mp.Vector3(0, 0, 0),
size=mp.Vector3(x_mon_prime, y_mon_prime, 0))
monitor_yz = mp.Volume(center=mp.Vector3(0, 0, 0),
size=mp.Vector3(0, y_mon_prime, z_mon_prime))
#Now make the simulation
sim = mp.Simulation(
cell_size=cell,
boundary_layers=pml_layers,
geometry=[],
sources=sources,
resolution=res,
symmetries=symmetry,
dimensions=3,
k_point=mp.Vector3(0, -1 * ky_prime, 0),
material_function=mat_func,
extra_materials=[mp.Medium(epsilon=eps_tip, mu=4, D_conductivity=1)],
verbose=True)
sim.run(mp.in_volume(
monitor_xy,
mp.to_appended(save_prefix + "E_xy",
mp.at_every(1 / fcen / sample, mp.output_efield))),
mp.in_volume(
monitor_yz,
mp.to_appended(
save_prefix + "E_yz",
mp.at_every(1 / fcen / sample, mp.output_efield))),
until=waves / fcen)