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Infinite rect lattices script multiple freqs etc. 

Former-commit-id: 8db37dfaf051abf1d6a542eb6ca9b40317848469
This commit is contained in:
Marek Nečada 2020-04-05 21:41:15 +03:00
parent 3f266f5501
commit 3458acca16
2 changed files with 175 additions and 53 deletions
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206
misc/infiniterectlat-scatter.py
View File

@ -1,13 +1,11 @@
#!/usr/bin/env python3
import math
pi = math.pi
from qpms.argproc import ArgParser
ap = ArgParser(['rectlattice2d', 'single_particle', 'single_lMax', 'single_omega'])
ap.add_argument("-k", '--kx-lim', nargs=2, type=float, required=True, help='k vector', metavar=('KX_MIN', 'KX_MAX'))
# ap.add_argument("--kpi", action='store_true', help="Indicates that the k vector is given in natural units instead of SI, i.e. the arguments given by -k shall be automatically multiplied by pi / period (given by -p argument)")
ap = ArgParser(['rectlattice2d', 'single_particle', 'single_lMax', 'omega_seq_real_ng', 'planewave'])
ap.add_argument("-o", "--output", type=str, required=False, help='output path (if not provided, will be generated automatically)')
ap.add_argument("-N", type=int, default="151", help="Number of angles")
ap.add_argument("-O", "--plot-out", type=str, required=False, help="path to plot output (optional)")
ap.add_argument("-P", "--plot", action='store_true', help="if -p not given, plot to a default path")
#ap.add_argument("-g", "--save-gradually", action='store_true', help="saves the partial result after computing each irrep")
@ -18,17 +16,9 @@ a=ap.parse_args()
import logging
logging.basicConfig(format='%(asctime)s %(message)s', level=logging.INFO)
px, py = a.period
particlestr = ("sph" if a.height is None else "cyl") + ("_r%gnm" % (a.radius*1e9))
if a.height is not None: particlestr += "_h%gnm" % (a.height * 1e9)
defaultprefix = "%s_p%gnmx%gnm_m%s_n%g_angles(%g_%g)_Ey_f%geV_L%d_cn%d" % (
particlestr, px*1e9, py*1e9, str(a.material), a.refractive_index, a.kx_lim[0], a.kx_lim[1], a.eV, a.lMax, a.N)
logging.info("Default file prefix: %s" % defaultprefix)
import numpy as np
import qpms
from qpms.qpms_p import cart2sph, sph2cart, sph_loccart2cart, sph_loccart_basis
import warnings
from qpms.cybspec import BaseSpec
from qpms.cytmatrices import CTMatrix, TMatrixGenerator
@ -40,6 +30,15 @@ eh = eV/hbar
dbgmsg_enable(DebugFlags.INTEGRATION)
px, py = a.period
particlestr = ("sph" if a.height is None else "cyl") + ("_r%gnm" % (a.radius*1e9))
if a.height is not None: particlestr += "_h%gnm" % (a.height * 1e9)
defaultprefix = "%s_p%gnmx%gnm_m%s_n%g_φ%g_θ(%g_%g)π_ψ%gπ_χ%gπ_f%s_L%d" % (
particlestr, px*1e9, py*1e9, str(a.material), a.refractive_index, a.phi/pi, np.amin(a.theta)/pi, np.amax(a.theta)/pi, a.psi/pi, a.chi/pi, ap.omega_descr, a.lMax)
logging.info("Default file prefix: %s" % defaultprefix)
a1 = ap.direct_basis[0]
a2 = ap.direct_basis[1]
@ -48,72 +47,173 @@ orig_x = [0]
orig_y = [0]
orig_xy = np.stack(np.meshgrid(orig_x,orig_y),axis=-1)
omega = ap.omega
bspec = BaseSpec(lMax = a.lMax)
# The parameters here should probably be changed (needs a better qpms_c.Particle implementation)
pp = Particle(orig_xy[0][0], ap.tmgen, bspec=bspec)
par = [pp]
ss, ssw = ScatteringSystem.create(par, ap.background_emg, omega, latticebasis = ap.direct_basis)
ss, ssw = ScatteringSystem.create(par, ap.background_emg, ap.allomegas[0], latticebasis = ap.direct_basis)
if ssw.wavenumber.imag != 0:
warnings.warn("The background medium wavenumber has non-zero imaginary part. Don't expect meaningful results for cross sections.")
wavenumber = ssw.wavenumber.real
sinalpha_list = np.linspace(a.kx_lim[0],a.kx_lim[1],a.N)
## Plane wave data
a.theta = np.array(a.theta)
dir_sph_list = np.stack((np.broadcast_to(1, a.theta.shape), a.theta, np.broadcast_to(a.phi, a.theta.shape)), axis=-1)
sψ, cψ = math.sin(a.psi), math.cos(a.psi)
sχ, cχ = math.sin(a.chi), math.cos(a.chi)
E_sph = (0., cψ*cχ + 1j*sψ*sχ, sψ*cχ + 1j*cψ*sχ)
# Plane wave data
E_cart_list = np.empty((a.N,3), dtype=complex)
E_cart_list[:,:] = np.array((0,1,0))[None,:]
k_cart_list = np.empty((a.N,3), dtype=float)
k_cart_list[:,0] = sinalpha_list
k_cart_list[:,1] = 0
k_cart_list[:,2] = np.sqrt(1-sinalpha_list**2)
k_cart_list *= wavenumber
dir_cart_list = sph2cart(dir_sph_list)
E_cart_list = sph_loccart2cart(E_sph, dir_sph_list)
σ_ext_list = np.empty((a.N,), dtype=float)
σ_scat_list = np.empty((a.N,), dtype=float)
nfreq = len(ap.allomegas)
ndir = len(dir_sph_list)
k_cart_arr = np.empty((nfreq, ndir, 3), dtype=float)
wavenumbers = np.empty((nfreq,), dtype=float)
σ_ext_arr = np.empty((nfreq,ndir), dtype=float)
σ_scat_arr = np.empty((nfreq,ndir), dtype=float)
with pgsl_ignore_error(15): # avoid gsl crashing on underflow
for j in range(a.N):
k_cart = k_cart_list[j]
blochvector = (k_cart[0], k_cart[1], 0)
# the following two could be calculated only once, but probably not a big deal
LU = ssw.scatter_solver(k=blochvector)
ã = ss.planewave_full(k_cart=k_cart, E_cart=E_cart_list[j])
Tã = ssw.apply_Tmatrices_full(ã)
f = LU(Tã)
for i, omega in enumerate(ap.allomegas):
if i != 0:
ssw = ss(omega)
if ssw.wavenumber.imag != 0:
warnings.warn("The background medium wavenumber has non-zero imaginary part. Don't expect meaningful results for cross sections.")
wavenumber = ssw.wavenumber.real
wavenumbers[i] = wavenumber
σ_ext_list[j] = -np.vdot(ã, f).real/wavenumber**2
translation_matrix = ssw.translation_matrix_full(blochvector=blochvector) + np.eye(ss.fecv_size)
σ_scat_list[j] = np.vdot(f,np.dot(translation_matrix, f)).real/wavenumber**2
k_sph_list = np.array(dir_sph_list, copy=True)
k_sph_list[:,0] = wavenumber
σ_abs_list = σ_ext_list - σ_scat_list
k_cart_arr[i] = sph2cart(k_sph_list)
for j in range(ndir):
k_cart = k_cart_arr[i,j]
blochvector = (k_cart[0], k_cart[1], 0)
# the following two could be calculated only once, but probably not a big deal
LU = ssw.scatter_solver(k=blochvector)
ã = ss.planewave_full(k_cart=k_cart, E_cart=E_cart_list[j])
Tã = ssw.apply_Tmatrices_full(ã)
f = LU(Tã)
σ_ext_arr[i,j] = -np.vdot(ã, f).real/wavenumber**2
translation_matrix = ssw.translation_matrix_full(blochvector=blochvector) + np.eye(ss.fecv_size)
σ_scat_arr[i,j] = np.vdot(f,np.dot(translation_matrix, f)).real/wavenumber**2
σ_abs_arr = σ_ext_arr - σ_scat_arr
outfile = defaultprefix + ".npz" if a.output is None else a.output
np.savez(outfile, meta=vars(a), sinalpha=sinalpha_list, k_cart = k_cart_list, E_cart=E_cart_list, σ_ext=σ_ext_list,σ_abs=σ_abs_list,σ_scat=σ_scat_list, omega=omega, wavenumber=wavenumber, unitcell_area=ss.unitcell_volume
np.savez(outfile, meta=vars(a), dir_sph=dir_sph_list, k_cart = k_cart_arr, omega = ap.allomegas, E_cart = E_cart_list, wavenumbers= wavenumbers, σ_ext=σ_ext_arr,σ_abs=σ_abs_arr,σ_scat=σ_scat_arr, unitcell_area=ss.unitcell_volume
)
logging.info("Saved to %s" % outfile)
if a.plot or (a.plot_out is not None):
import matplotlib
from matplotlib.backends.backend_pdf import PdfPages
matplotlib.use('pdf')
from matplotlib import pyplot as plt
from scipy.interpolate import griddata
fig = plt.figure()
ax = fig.add_subplot(111)
ax.plot(sinalpha_list, σ_ext_list*1e12,label='$\sigma_\mathrm{ext}$')
ax.plot(sinalpha_list, σ_scat_list*1e12, label='$\sigma_\mathrm{scat}$')
ax.plot(sinalpha_list, σ_abs_list*1e12, label='$\sigma_\mathrm{abs}$')
ax.legend()
ax.set_xlabel('$\sin\\alpha$')
ax.set_ylabel('$\sigma/\mathrm{\mu m^2}$')
plotfile = defaultprefix + ".pdf" if a.plot_out is None else a.plot_out
fig.savefig(plotfile)
with PdfPages(plotfile) as pdf:
ipm = 'nearest'
sintheta = np.sin(a.theta)
if False: #len(ap.omega_ranges) != 0:
# angle plot ---------------------------------
fig = plt.figure(figsize=(210/25.4, 297/25.4))
vmax = max(np.amax(σ_ext_arr), np.amax(σ_scat_arr), np.amax(σ_abs_arr))
vmin = min(np.amin(σ_ext_arr), np.amin(σ_scat_arr), np.amin(σ_abs_arr))
ax = fig.add_subplot(311)
ax.pcolormesh(a.theta, ap.allomegas/eh, σ_ext_arr, vmin=vmin, vmax=vmax)
ax.set_xlabel('$\\theta$')
ax.set_ylabel('$\\hbar\\omega / \\mathrm{eV}$')
ax.set_title('$\\sigma_\\mathrm{ext}$')
ax = fig.add_subplot(312)
ax.pcolormesh(a.theta, ap.allomegas/eh, σ_scat_arr, vmin=vmin, vmax=vmax)
ax.set_xlabel('$\\theta$')
ax.set_ylabel('$\\hbar\\omega / \\mathrm{eV}$')
ax.set_title('$\\sigma_\\mathrm{scat}$')
ax = fig.add_subplot(313)
im = ax.pcolormesh(a.theta, ap.allomegas/eh, σ_abs_arr, vmin=vmin, vmax=vmax)
ax.set_xlabel('$\\theta$')
ax.set_ylabel('$\\hbar\\omega / \\mathrm{eV}$')
ax.set_title('$\\sigma_\\mathrm{abs}$')
fig.subplots_adjust(right=0.8)
fig.colorbar(im, cax = fig.add_axes([0.85, 0.15, 0.05, 0.7]))
pdf.savefig(fig)
plt.close(fig)
if len(ap.omega_ranges) != 0:
# "k-space" plot -----------------------------
domega = np.amin(np.diff(ap.allomegas))
dsintheta = np.amin(abs(np.diff(sintheta)))
dk = dsintheta * wavenumbers[0]
# target image grid
grid_y, grid_x = np.mgrid[ap.allomegas[0] : ap.allomegas[-1] : domega, np.amin(sintheta) * wavenumbers[-1] : np.amax(sintheta) * wavenumbers[-1] : dk]
imextent = (np.amin(sintheta) * wavenumbers[-1] / 1e6, np.amax(sintheta) * wavenumbers[-1] / 1e6, ap.allomegas[0] / eh, ap.allomegas[-1] / eh)
# source coordinates for griddata
ktheta = sintheta[None, :] * wavenumbers[:, None]
omegapoints = np.broadcast_to(ap.allomegas[:, None], ktheta.shape)
points = np.stack( (ktheta.flatten(), omegapoints.flatten()), axis = -1)
fig = plt.figure(figsize=(210/25.4, 297/25.4))
vmax = np.amax(σ_ext_arr)
ax = fig.add_subplot(311)
grid_z = griddata(points, σ_ext_arr.flatten(), (grid_x, grid_y), method = ipm)
ax.imshow(grid_z, extent = imextent, origin = 'lower', vmin = 0, vmax = vmax, aspect = 'auto', interpolation='none')
ax.set_xlabel('$k_\\theta / \\mathrm{\\mu m^{-1}}$')
ax.set_ylabel('$\\hbar\\omega / \\mathrm{eV}$')
ax.set_title('$\\sigma_\\mathrm{ext}$')
ax = fig.add_subplot(312)
grid_z = griddata(points, σ_scat_arr.flatten(), (grid_x, grid_y), method = ipm)
ax.imshow(grid_z, extent = imextent, origin = 'lower', vmin = 0, vmax = vmax, aspect = 'auto', interpolation='none')
ax.set_xlabel('$k_\\theta / \\mathrm{\\mu m^{-1}}$')
ax.set_ylabel('$\\hbar\\omega / \\mathrm{eV}$')
ax.set_title('$\\sigma_\\mathrm{scat}$')
ax = fig.add_subplot(313)
grid_z = griddata(points, σ_abs_arr.flatten(), (grid_x, grid_y), method = ipm)
im = ax.imshow(grid_z, extent = imextent, origin = 'lower', vmin = 0, vmax = vmax, aspect = 'auto', interpolation='none')
ax.set_xlabel('$k_\\theta / \\mathrm{\\mu m^{-1}}$')
ax.set_ylabel('$\\hbar\\omega / \\mathrm{eV}$')
ax.set_title('$\\sigma_\\mathrm{abs}$')
fig.subplots_adjust(right=0.8)
fig.colorbar(im, cax = fig.add_axes([0.85, 0.15, 0.05, 0.7]))
pdf.savefig(fig)
plt.close(fig)
for omega in ap.omega_singles:
i = np.searchsorted(ap.allomegas, omega)
fig = plt.figure()
fig.suptitle("%g eV" % (omega / eh))
ax = fig.add_subplot(111)
sintheta = np.sin(a.theta)
ax.plot(sintheta, σ_ext_arr[i]*1e12,label='$\sigma_\mathrm{ext}$')
ax.plot(sintheta, σ_scat_arr[i]*1e12, label='$\sigma_\mathrm{scat}$')
ax.plot(sintheta, σ_abs_arr[i]*1e12, label='$\sigma_\mathrm{abs}$')
ax.legend()
ax.set_xlabel('$\sin\\theta$')
ax.set_ylabel('$\sigma/\mathrm{\mu m^2}$')
pdf.savefig(fig)
plt.close(fig)
exit(0)

22
qpms/argproc.py
View File

@ -93,6 +93,7 @@ class ArgParser:
'single_frequency_eV': lambda ap: ap.add_argument("-f", "--eV", type=float, required=True, help='radiation angular frequency in eV'),
'multiple_frequency_eV_optional': lambda ap: ap.add_argument("-f", "--eV", type=float, nargs='*', help='radiation angular frequency in eV (additional)'),
'seq_frequency_eV': lambda ap: ap.add_argument("-F", "--eV-seq", type=float, nargs=3, required=True, help='uniform radiation angular frequency sequence in eV', metavar=('FIRST', 'INCREMENT', 'LAST')),
'real_frequencies_eV_ng': lambda ap: ap.add_argument("-f", "--eV", type=float_range, nargs='+', required=True, help='Angular frequency (or angular frequency range) in eV'),
'single_material': lambda ap: ap.add_argument("-m", "--material", help='particle material (Au, Ag, ... for Lorentz-Drude or number for constant refractive index)', default='Au', required=True),
'single_radius': lambda ap: ap.add_argument("-r", "--radius", type=float, required=True, help='particle radius (sphere or cylinder)'),
'single_height': lambda ap: ap.add_argument("-H", "--height", type=float, help='cylindrical particle height; if not provided, particle is assumed to be spherical'),
@ -114,6 +115,7 @@ class ArgParser:
'single_lMax': ("Single particle lMax definition", (), ('single_lMax',), ()),
'single_omega': ("Single angular frequency", (), ('single_frequency_eV',), ('_eval_single_omega',)),
'omega_seq': ("Equidistant real frequency range with possibility of adding individual frequencies", (), ('seq_frequency_eV', 'multiple_frequency_eV_optional',), ('_eval_omega_seq',)),
'omega_seq_real_ng': ("Equidistant real frequency ranges or individual frequencies (new syntax)", (), ('real_frequencies_eV_ng',), ('_eval_omega_seq_real_ng',)),
'lattice2d': ("Specification of a generic 2d lattice (spanned by the x,y axes)", (), ('lattice2d_basis',), ('_eval_lattice2d',)),
'rectlattice2d': ("Specification of a rectangular 2d lattice; conflicts with lattice2d", (), ('rectlattice2d_periods',), ('_eval_rectlattice2d',)),
'rectlattice2d_finite': ("Specification of a rectangular 2d lattice; conflicts with lattice2d", ('rectlattice2d',), ('rectlattice2d_counts',), ()),
@ -199,6 +201,26 @@ class ArgParser:
self.omegas.sort()
self.omegas *= eV/hbar
def _eval_omega_seq_real_ng(self): # feature: omega_seq_real_ng
import numpy as np
from .constants import eV, hbar
eh = eV / hbar
self.omegas = [omega_eV * eh for omega_eV in self.args.eV]
self.omega_max = max(om if isinstance(om, float) else max(om) for om in self.omegas)
self.omega_min = min(om if isinstance(om, float) else min(om) for om in self.omegas)
self.omega_singles = [om for om in self.omegas if isinstance(om, float)]
self.omega_ranges = [om for om in self.omegas if not isinstance(om, float)]
self.omega_descr = ("%geV" % (self.omega_max / eh)) if (self.omega_max == self.omega_min) else (
"%g–%geV" % (self.omega_min / eh, self.omega_max / eh))
self.allomegas = []
for om in self.omegas:
if isinstance(om, float):
self.allomegas.append(om)
else:
self.allomegas.extend(om)
self.allomegas = np.unique(self.allomegas)
def _eval_lattice2d(self): # feature: lattice2d
l = len(self.args.basis_vectors)
if l != 2: raise ValueError('Two basis vectors must be specified (have %d)' % l)