From 3da6e5cfb2ab7c2d5c9bb3219044fd9765ad5958 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marek=20Ne=C4=8Dada?= Date: Tue, 7 Apr 2020 21:01:18 +0300 Subject: [PATCH] WIP argproc multiparticle; update misc scripts Former-commit-id: 50986e9e57873f8aca1ec7a8aafaa659434a839f --- misc/finiterectlat-scatter.py | 229 ++++++++++++++++++------- misc/infiniterectlat-scatter.py | 4 +- misc/rectlat_simple_modes.py | 2 +- qpms/argproc.py | 291 +++++++++++++++++++++++++++----- qpms/qpms_c.pyx | 7 +- 5 files changed, 421 insertions(+), 112 deletions(-) diff --git a/misc/finiterectlat-scatter.py b/misc/finiterectlat-scatter.py index 485ef22..98a3f30 100755 --- a/misc/finiterectlat-scatter.py +++ b/misc/finiterectlat-scatter.py @@ -1,10 +1,11 @@ #!/usr/bin/env python3 import math +pi = math.pi from qpms.argproc import ArgParser -ap = ArgParser(['rectlattice2d_finite', 'single_particle', 'single_lMax', 'single_omega', 'planewave']) +ap = ArgParser(['rectlattice2d_finite', '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("-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") @@ -16,13 +17,8 @@ a=ap.parse_args() import logging logging.basicConfig(format='%(asctime)s %(message)s', level=logging.INFO) -Nx, Ny = a.size -px, py = a.period - - import numpy as np import qpms -import math from qpms.qpms_p import cart2sph, sph2cart, sph_loccart2cart, sph_loccart_basis from qpms.cybspec import BaseSpec from qpms.cytmatrices import CTMatrix, TMatrixGenerator @@ -32,15 +28,18 @@ from qpms.cycommon import DebugFlags, dbgmsg_enable from qpms import FinitePointGroup, ScatteringSystem, BesselType, eV, hbar from qpms.symmetries import point_group_info eh = eV/hbar -pi = math.pi + +dbgmsg_enable(DebugFlags.INTEGRATION) + +Nx, Ny = a.size +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_%dx%d_m%s_n%g_φ%gπ_θ(%g_%g)π_ψ%gπ_χ%gπ_f%geV_L%d" % ( - particlestr, px*1e9, py*1e9, Nx, Ny, 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, a.eV, a.lMax, ) +defaultprefix = "%s_p%gnmx%gnm_%dx%d_m%s_bg%s_φ%gπ_θ(%g_%g)π_ψ%gπ_χ%gπ_f%s_L%d" % ( + particlestr, px*1e9, py*1e9, Nx, Ny, str(a.material), str(a.background), 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) -dbgmsg_enable(DebugFlags.INTEGRATION) #Particle positions orig_x = (np.arange(Nx/2) + (0 if (Nx % 2) else .5)) * px @@ -48,91 +47,191 @@ orig_y = (np.arange(Ny/2) + (0 if (Ny % 2) else .5)) * py orig_xy = np.stack(np.meshgrid(orig_x, orig_y), axis = -1) - -omega = ap.omega - bspec = BaseSpec(lMax = a.lMax) -Tmatrix = ap.tmgen(bspec, ap.omega) -particles= [Particle(orig_xy[i], Tmatrix) for i in np.ndindex(orig_xy.shape[:-1])] +particles= [Particle(orig_xy[i], ap.tmgen, bspec=bspec) for i in np.ndindex(orig_xy.shape[:-1])] sym = FinitePointGroup(point_group_info['D2h']) -ss, ssw = ScatteringSystem.create(particles, ap.background_emg, omega, sym=sym) +ss, ssw = ScatteringSystem.create(particles, ap.background_emg, ap.allomegas[0], sym=sym) -wavenumber = ap.background_epsmu.k(omega).real # Currently, ScatteringSystem does not "remember" frequency nor wavenumber ## Plane wave data -a.theta = np.array(a.theta) -k_sph_list = np.stack((np.broadcast_to(wavenumber, a.theta.shape), a.theta, np.broadcast_to(a.phi, a.theta.shape)), axis=-1) +a.theta = np.atleast_1d(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) -k_cart_list = sph2cart(k_sph_list) -E_cart_list = sph_loccart2cart(E_sph, k_sph_list) +dir_cart_list = sph2cart(dir_sph_list) +E_cart_list = sph_loccart2cart(E_sph, dir_sph_list) -npoints = a.theta.shape[0] +nfreq = len(ap.allomegas) +ndir = a.theta.shape[0] -σ_ext_list_ir = np.empty((npoints, ss.nirreps), dtype=float) -σ_scat_list_ir = np.empty((npoints, ss.nirreps), dtype=float) +k_cart_arr = np.empty((nfreq, ndir, 3), dtype=float) +wavenumbers = np.empty((nfreq,), dtype=float) + +σ_ext_arr_ir = np.empty((nfreq, ndir, ss.nirreps), dtype=float) +σ_scat_arr_ir = np.empty((nfreq, ndir, ss.nirreps), dtype=float) outfile_tmp = defaultprefix + ".tmp" if a.output is None else a.output + ".tmp" -for iri in range(ss.nirreps): - logging.info("processing irrep %d/%d" % (iri, ss.nirreps)) - LU = None # to trigger garbage collection before the next call - translation_matrix = None - LU = ssw.scatter_solver(iri) - logging.info("LU solver created") - translation_matrix = ss.translation_matrix_packed(wavenumber, iri, BesselType.REGULAR) + np.eye(ss.saecv_sizes[iri]) - logging.info("auxillary translation matrix created") +for i, omega in enumerate(ap.allomegas): + logging.info("Processing frequency %g eV" % (omega / eV,)) + 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 emaningful results for cross sections.") + wavenumber = ssw.wavenumber.real + wavenumbers[i] = wavenumber - for j in range(npoints): - # the following two could be calculated only once, but probably not a big deal - ã = ss.planewave_full(k_cart=k_cart_list[j], E_cart=E_cart_list[j]) - Tã = ssw.apply_Tmatrices_full(ã) + k_sph_list = np.array(dir_sph_list, copy=True) + k_sph_list[:,0] = wavenumber - Tãi = ss.pack_vector(Tã, iri) - ãi = ss.pack_vector(ã, iri) - fi = LU(Tãi) - σ_ext_list_ir[j, iri] = -np.vdot(ãi, fi).real/wavenumber**2 - σ_scat_list_ir[j, iri] = np.vdot(fi,np.dot(translation_matrix, fi)).real/wavenumber**2 - if a.save_gradually: - iriout = outfile_tmp + ".%d" % iri - np.savez(iriout, iri=iri, meta=vars(a), k_sph=k_sph_list, k_cart = k_cart_list, E_cart=E_cart_list, E_sph=np.array(E_sph), - omega=omega, wavenumber=wavenumber, σ_ext_list_ir=σ_ext_list_ir[:,iri], σ_scat_list_ir=σ_scat_list_ir[:,iri]) - logging.info("partial results saved to %s"%iriout) + k_cart_arr[i] = sph2cart(k_sph_list) -σ_abs_list_ir = σ_ext_list_ir - σ_scat_list_ir -σ_abs= np.sum(σ_abs_list_ir, axis=-1) -σ_scat= np.sum(σ_scat_list_ir, axis=-1) -σ_ext= np.sum(σ_ext_list_ir, axis=-1) + for iri in range(ss.nirreps): + logging.info("processing irrep %d/%d" % (iri, ss.nirreps)) + LU = None # to trigger garbage collection before the next call + translation_matrix = None + LU = ssw.scatter_solver(iri) + logging.info("LU solver created") + translation_matrix = ssw.translation_matrix_packed(iri, BesselType.REGULAR) + np.eye(ss.saecv_sizes[iri]) + logging.info("auxillary translation matrix created") + + for j in range(ndir): + k_cart = k_cart_arr[i,j] + # the following two could be calculated only once, but probably not a big deal + ã = ss.planewave_full(k_cart=k_cart_arr[i,j], E_cart=E_cart_list[j]) + Tã = ssw.apply_Tmatrices_full(ã) + + Tãi = ss.pack_vector(Tã, iri) + ãi = ss.pack_vector(ã, iri) + fi = LU(Tãi) + σ_ext_arr_ir[i, j, iri] = -np.vdot(ãi, fi).real/wavenumber**2 + σ_scat_arr_ir[i, j, iri] = np.vdot(fi,np.dot(translation_matrix, fi)).real/wavenumber**2 + if a.save_gradually: + iriout = outfile_tmp + ".%d.%d" % (i, iri) + np.savez(iriout, omegai=i, iri=iri, meta=vars(a), omega=omega, k_sph=k_sph_list, k_cart = k_cart_arr, E_cart=E_cart_list, E_sph=np.array(E_sph), + wavenumber=wavenumber, σ_ext_list_ir=σ_ext_arr_ir[i,:,iri], σ_scat_list_ir=σ_scat_list_ir[i,:,iri]) + logging.info("partial results saved to %s"%iriout) + +σ_abs_arr_ir = σ_ext_arr_ir - σ_scat_arr_ir +σ_abs_arr = np.sum(σ_abs_arr_ir, axis=-1) +σ_scat_arr = np.sum(σ_scat_arr_ir, axis=-1) +σ_ext_arr = np.sum(σ_ext_arr_ir, axis=-1) outfile = defaultprefix + ".npz" if a.output is None else a.output -np.savez(outfile, meta=vars(a), k_sph=k_sph_list, k_cart = k_cart_list, E_cart=E_cart_list, E_sph=np.array(E_sph), - σ_ext=σ_ext,σ_abs=σ_abs,σ_scat=σ_scat, - σ_ext_ir=σ_ext_list_ir,σ_abs_ir=σ_abs_list_ir,σ_scat_ir=σ_scat_list_ir, omega=omega, wavenumber=wavenumber +np.savez(outfile, meta=vars(a), k_sph=k_sph_list, k_cart = k_cart_arr, E_cart=E_cart_list, E_sph=np.array(E_sph), + σ_ext=σ_ext_arr,σ_abs=σ_abs_arr,σ_scat=σ_scat_arr, + σ_ext_ir=σ_ext_arr_ir,σ_abs_ir=σ_abs_arr_ir,σ_scat_ir=σ_scat_arr_ir, omega=ap.allomegas, wavenumbers=wavenumbers ) 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) - sintheta = np.sin(a.theta) - ax.plot(sintheta, σ_ext*1e12,label='$\sigma_\mathrm{ext}$') - ax.plot(sintheta, σ_scat*1e12, label='$\sigma_\mathrm{scat}$') - ax.plot(sintheta, σ_abs*1e12, label='$\sigma_\mathrm{abs}$') - ax.legend() - ax.set_xlabel('$\sin\\theta$') - 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) diff --git a/misc/infiniterectlat-scatter.py b/misc/infiniterectlat-scatter.py index b7111b6..9caa0de 100755 --- a/misc/infiniterectlat-scatter.py +++ b/misc/infiniterectlat-scatter.py @@ -34,8 +34,8 @@ 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) +defaultprefix = "%s_p%gnmx%gnm_m%s_bg%s_φ%g_θ(%g_%g)π_ψ%gπ_χ%gπ_f%s_L%d" % ( + particlestr, px*1e9, py*1e9, str(a.material), str(a.background), 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) diff --git a/misc/rectlat_simple_modes.py b/misc/rectlat_simple_modes.py index fa614e2..4029066 100755 --- a/misc/rectlat_simple_modes.py +++ b/misc/rectlat_simple_modes.py @@ -3,7 +3,7 @@ import math from qpms.argproc import ArgParser -ap = ArgParser(['rectlattice2d', 'single_particle', 'single_lMax']) +ap = ArgParser(['rectlattice2d', 'const_real_background', 'single_particle', 'single_lMax']) # const_real_background needed for calculation of the diffracted orders ap.add_argument("-k", nargs=2, type=float, required=True, help='k vector', metavar=('K_X', 'K_Y')) 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.add_argument("--rank-tol", type=float, required=False) diff --git a/qpms/argproc.py b/qpms/argproc.py index 6942dbd..f97e3ba 100644 --- a/qpms/argproc.py +++ b/qpms/argproc.py @@ -4,6 +4,14 @@ Common snippets for argument processing in command line scripts; legacy scripts import argparse import sys +import warnings + +def flatten(S): + if S == []: + return S + if isinstance(S[0], list): + return flatten(S[0]) + flatten(S[1:]) + return S[:1] + flatten(S[1:]) def make_action_sharedlist(opname, listname): class opAction(argparse.Action): @@ -13,6 +21,40 @@ def make_action_sharedlist(opname, listname): getattr(args, listname).append((opname, values)) return opAction +def make_dict_action(argtype=None, postaction='store', first_is_key=True): + class DictAction(argparse.Action): + #def __init__(self, option_strings, dest, nargs=None, **kwargs): + # if nargs is not None: + # raise ValueError("nargs not allowed") + # super(DictAction, self).__init__(option_strings, dest, **kwargs) + def __call__(self, parser, namespace, values, option_string=None): + if first_is_key: # For the labeled versions + key = values[0] + vals = values[1:] + else: # For the default values + key = None + vals = values + if argtype is not None: + if (first_is_key and self.nargs == 2) or (not first_is_key and self.nargs == 1): + vals = argtype(vals[0]) # avoid having lists in this case + else: + vals = [argtype(val) for val in vals] + ledict = getattr(namespace, self.dest, {}) + if ledict is None: + ledict = {} + if postaction=='store': + ledict[key] = vals + elif postaction=='append': + lelist = ledict.get(key, []) + lelist.append(vals) + ledict[key] = lelist + setattr(namespace, self.dest, ledict) + return DictAction + + +class ArgumentProcessingError(Exception): + pass + class AppendTupleAction(argparse.Action): ''' A variation on the 'append' builtin action from argparse, but uses tuples for the internal groupings instead of lists ''' def __call__(self, parser, args, values, option_string=None): @@ -39,17 +81,14 @@ def float_range(string): steps = None match = re.match(r's?([^:]+):([^|]+)\|(.+)', string) if match: - #print("first:last|steps", match.group(1,2,3)) steps = int(match.group(3)) else: match = re.match(r's?([^:]+):([^:]+):(.+)', string) if match: - #print("first:last:increment", match.group(1,2,3)) increment = float(match.group(3)) else: match = re.match(r's?([^:]+):(.+)', string) if match: - #print("first:last", match.group(1,2)) steps = 50 else: argparse.ArgumentTypeError('Invalid float/sequence format: "%s"' % string) @@ -61,6 +100,24 @@ def float_range(string): else: return np.arange(first, last, increment) +def material_spec(string): + """Tries to parse a string as a material specification, i.e. a + real or complex number or one of the string in built-in Lorentz-Drude models. + + Tries to interpret the string as 1) float, 2) complex, 3) Lorentz-Drude key. + Raises argparse.ArgumentTypeError on failure. + """ + from .cymaterials import lorentz_drude + if string in lorentz_drude.keys(): + return string + else: + try: lemat = float(string) + except ValueError: + try: lemat = complex(string) + except ValueError as ve: + raise argpares.ArgumentTypeError("Material specification must be a supported material name %s, or a number" % (str(lorentz_drude.keys()),)) from ve + return lemat + class ArgParser: ''' Common argument parsing engine for QPMS python CLI scripts. ''' @@ -87,56 +144,143 @@ class ArgParser: pwgrp.add_argument("-χ", "--chi", type=float, default=0, help='Polarisation parameter χ in multiples of π/2. 0 for linear, 0.5 for circular pol.') + def __add_manyparticle_argparse_group(ap): + mpgrp = ap.add_argument_group('Many particle specification', "TODO DOC") + mpgrp.add_argument("-p", "--position", nargs='+', action=make_dict_action(argtype=float, postaction='append', + first_is_key=False), help="Particle positions, cartesion coordinates (default particle properties)") + mpgrp.add_argument("+p", "++position", nargs='+', action=make_dict_action(argtype=float, postaction='append', + first_is_key=True), help="Particle positions, cartesian coordinates (labeled)") + mpgrp.add_argument("-L", "--lMax", nargs=1, default={}, + action=make_dict_action(argtype=int, postaction='store', first_is_key=False,), + help="Cutoff multipole degree (default)") + mpgrp.add_argument("+L", "++lMax", nargs=2, + action=make_dict_action(argtype=int, postaction='store', first_is_key=True,), + help="Cutoff multipole degree (labeled)") + mpgrp.add_argument("-m", "--material", nargs=1, default={}, + action=make_dict_action(argtype=material_spec, postaction='store', first_is_key=False,), + help='particle material (Au, Ag, ... for Lorentz-Drude or number for constant refractive index) (default)') + mpgrp.add_argument("+m", "++material", nargs=2, + action=make_dict_action(argtype=material_spec, postaction='store', first_is_key=True,), + help='particle material (Au, Ag, ... for Lorentz-Drude or number for constant refractive index) (labeled)') + mpgrp.add_argument("-r", "--radius", nargs=1, default={}, + action=make_dict_action(argtype=float, postaction='store', first_is_key=False,), + help='particle radius (sphere or cylinder; default)') + mpgrp.add_argument("+r", "++radius", nargs=2, + action=make_dict_action(argtype=float, postaction='store', first_is_key=True,), + help='particle radius (sphere or cylinder; labeled)') + mpgrp.add_argument("-H", "--height", nargs=1, default={}, + action=make_dict_action(argtype=float, postaction='store', first_is_key=False,), + help='particle radius (cylinder; default)') + mpgrp.add_argument("+H", "++height", nargs=2, + action=make_dict_action(argtype=float, postaction='store', first_is_key=True,), + help='particle radius (cylinder; labeled)') + atomic_arguments = { 'rectlattice2d_periods': lambda ap: ap.add_argument("-p", "--period", type=float, nargs='+', required=True, help='square/rectangular lattice periods', metavar=('px','[py]')), 'rectlattice2d_counts': lambda ap: ap.add_argument("--size", type=int, nargs=2, required=True, help='rectangular array size (particle column, row count)', metavar=('NCOLS', 'NROWS')), '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), + 'real_frequencies_eV_ng': lambda ap: ap.add_argument("-f", "--eV", type=float_range, nargs=1, action='append', required=True, help='Angular frequency (or angular frequency range) in eV'), # nargs='+', action='extend' would be better, but action='extend' requires python>=3.8 + 'single_material': lambda ap: ap.add_argument("-m", "--material", help='particle material (Au, Ag, ... for Lorentz-Drude or number for constant refractive index)', type=material_spec, 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'), 'single_kvec2': lambda ap: ap.add_argument("-k", '--kx-lim', nargs=2, type=float, required=True, help='k vector', metavar=('KX_MIN', 'KX_MAX')), 'kpi': lambda ap: 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)"), - 'bg_refractive_index': lambda ap: ap.add_argument("-n", "--refractive-index", type=float, default=1.52, help='background medium refractive index'), + 'bg_real_refractive_index': lambda ap: ap.add_argument("-n", "--refractive-index", type=float, default=1., help='background medium strictly real refractive index'), + 'bg_analytical': lambda ap: ap.add_argument("-B", "--background", type=material_spec, default=1., help="Background medium specification (constant real or complex refractive index, or supported material label)"), 'single_lMax': lambda ap: ap.add_argument("-L", "--lMax", type=int, required=True, default=3, help='multipole degree cutoff'), 'single_lMax_extend': lambda ap: ap.add_argument("--lMax-extend", type=int, required=False, default=6, help='multipole degree cutoff for T-matrix calculation (cylindrical particles only'), 'outfile': lambda ap: ap.add_argument("-o", "--output", type=str, required=False, help='output path (if not provided, will be generated automatically)'), # TODO consider type=argparse.FileType('w') 'plot_out': lambda ap: ap.add_argument("-O", "--plot-out", type=str, required=False, help="path to plot output (optional)"), 'plot_do': lambda ap: ap.add_argument("-P", "--plot", action='store_true', help="if -p not given, plot to a default path"), - 'lattice2d_basis': lambda ap: ap.add_argument("-b", "--basis-vector", action=AppendTupleAction, help="basis vector in xy-cartesian coordinates (two required)", dest='basis_vectors', metavar=('X', 'Y')), + 'lattice2d_basis': lambda ap: ap.add_argument("-b", "--basis-vector", nargs='+', action=AppendTupleAction, help="basis vector in xy-cartesian coordinates (two required)", required=True, dest='basis_vectors', metavar=('X', 'Y')), 'planewave_pol_angles': __add_planewave_argparse_group, + 'multi_particle': __add_manyparticle_argparse_group, } - feature_sets_available = { # name : (description, dependencies, atoms not in other dependencies, methods called after parsing) - 'background': ("Background medium definition (currently only constant epsilon supported)", (), ('bg_refractive_index',), ('_eval_background_epsmu',)), - 'single_particle': ("Single particle definition (shape [currently spherical or cylindrical]) and materials, incl. background)", ('background',), ('single_material', 'single_radius', 'single_height', 'single_lMax_extend'), ('_eval_single_tmgen',)), - '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',), ()), - 'planewave': ("Specification of a normalised plane wave (typically used for scattering) with a full polarisation state", (), ('planewave_pol_angles',), ("_process_planewave_angles",)), + feature_sets_available = { # name : (description, dependencies, atoms not in other dependencies, methods called after parsing, "virtual" features provided) + 'const_real_background': ("Background medium with constant real refractive index", (), ('bg_real_refractive_index',), ('_eval_const_background_epsmu',), ('background', 'background_analytical')), + 'background' : ("Most general background medium specification currently supported", ('background_analytical',), (), (), ()), + 'background_analytical' : ("Background medium model holomorphic for 'reasonably large' complex frequency areas", (), ('bg_analytical',), ('_eval_analytical_background_epsmugen',), ('background',)), + 'single_particle': ("Single particle definition (shape [currently spherical or cylindrical]) and materials, incl. background)", ('background',), ('single_material', 'single_radius', 'single_height', 'single_lMax_extend'), ('_eval_single_tmgen',), ()), + 'multi_particle': ("One or more particle definition (shape [curently spherical or cylindrical]), materials, and positions)", ('background',), ('multi_particle',), ('_process_multi_particle',), ()), + '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',), (), ()), + 'planewave': ("Specification of a normalised plane wave (typically used for scattering) with a full polarisation state", (), ('planewave_pol_angles',), ("_process_planewave_angles",), ()), } def __init__(self, features=[]): - self.ap = argparse.ArgumentParser() + prefix_chars = '+-' if 'multi_particle' in features else '-' + self.ap = argparse.ArgumentParser(prefix_chars=prefix_chars) self.features_enabled = set() self.call_at_parse_list = [] self.parsed = False for feat in features: self.add_feature(feat) + self._emg_register = {} # EpsMuGenerator dictionary to avoid recreating equivalent instances; filled by _add_emg() + self._tmg_register = {} # TMatrixGenerator dictionary to avoid recreating equivalent instances; filled by _add_tmg() + self._bspec_register = {} # Dictionary of used BaseSpecs to keep the equivalent instances unique; filled by _add_bspec() + + def _add_emg(self, emgspec): + """Looks up whether if an EpsMuGenerator from given material_spec has been already registered, and if not, creates a new one""" + from .cymaterials import EpsMu, EpsMuGenerator, lorentz_drude + if emgspec in self._emg_register.keys(): + return self._emg_register[emgspec] + else: + if isinstance(emgspec, (float, complex)): + emg = EpsMuGenerator(EpsMu(emgspec**2)) + else: + emg = EpsMuGenerator(lorentz_drude[emgspec]) + self._emg_register[emgspec] = emg + return emg + + def _add_tmg(self, tmgspec): + """Looks up whether if a T-matrix from given T-matrix specification tuple has been already registered, and if not, creates a new one + + T-matrix specification shall be of the form + (bg_material_spec, fg_material_spec, shape_spec) where shape_spec is + (radius, height, lMax_extend) + """ + if tmgspec in self._tmg_register.keys(): + return self._tmg_register[tmgspec] + else: + from .cytmatrices import TMatrixGenerator + bgspec, fgspec, (radius, height, lMax_extend) = tmgspec + bg = self._add_emg(bgspec) + fg = self._add_emg(fgspec) + if height is None: + tmgen = TMatrixGenerator.sphere(bg, fg, radius) + else: + tmgen = TMatrixGenerator.cylinder(bg, fg, radius, height, lMax_extend=lMax_extend) + self._tmg_register[tmgspec] = tmgen + return tmgen + + def _add_bspec(self, key): + if key in self._bspec_register.keys(): + return self._bspec_register[key] + else: + from .cybspec import BaseSpec + if isinstance(key, BaseSpec): + bspec = key + elif isinstance(key, int): + bspec = self._add_bspec(BaseSpec(lMax=key)) + else: raise TypeError("Can't register this as a BaseSpec") + self._bspec_register[key] = bspec + return bspec def add_feature(self, feat): if feat not in self.features_enabled: if feat not in ArgParser.feature_sets_available: raise ValueError("Unknown ArgParser feature: %s" % feat) #resolve dependencies - _, deps, atoms, atparse = ArgParser.feature_sets_available[feat] + _, deps, atoms, atparse, provides_virtual = ArgParser.feature_sets_available[feat] for dep in deps: self.add_feature(dep) for atom in atoms: # maybe check whether that atom has already been added sometimes in the future? @@ -144,6 +288,8 @@ class ArgParser: for methodname in atparse: self.call_at_parse_list.append(methodname) self.features_enabled.add(feat) + for feat_virt in provides_virtual: + self.features_enabled.add(feat_virt) def add_argument(self, *args, **kwargs): '''Add a custom argument directly to the standard library ArgParser object''' @@ -153,7 +299,11 @@ class ArgParser: self.args = self.ap.parse_args(*args, **kwargs) if process_data: for method in self.call_at_parse_list: - getattr(self, method)() + try: + getattr(self, method)() + except ArgumentProcessingError: + err = sys.exc_info()[1] + self.ap.error(str(err)) return self.args def __getattr__(self, name): @@ -162,30 +312,24 @@ class ArgParser: # Methods to initialise the related data structures: - def _eval_background_epsmu(self): # feature: background - from .cymaterials import EpsMu, EpsMuGenerator - self.background_epsmu = EpsMu(self.args.refractive_index**2) - self.background_emg = EpsMuGenerator(self.background_epsmu) + def _eval_const_background_epsmu(self): # feature: const_real_background + self.args.background = self.args.refractive_index + self._eval_analytical_background_epsmugen() + + def _eval_analytical_background_epsmugen(self): # feature: background_analytical + a = self.args + from .cymaterials import EpsMu + if isinstance(a.background, (float, complex)): + self.background_epsmu = EpsMu(a.background**2) + self.background_emg = self._add_emg(a.background) def _eval_single_tmgen(self): # feature: single_particle a = self.args from .cymaterials import EpsMuGenerator, lorentz_drude from .cytmatrices import TMatrixGenerator - if a.material in lorentz_drude.keys(): - self.foreground_emg = EpsMuGenerator(lorentz_drude[a.material]) - else: - try: lemat = float(a.material) - except ValueError: - try: lemat = complex(a.material) - except ValueError as ve: - raise ValueError("--material must be either a label such as 'Ag', 'Au', or a number") from ve - a.material = lemat - self.foreground_emg = EpsMuGenerator(EpsMu(a.material**2)) - - if a.height is None: - self.tmgen = TMatrixGenerator.sphere(self.background_emg, self.foreground_emg, a.radius) - else: - self.tmgen = TMatrixGenerator.cylinder(self.background_emg, self.foreground_emg, a.radius, a.height, lMax_extend = a.lMax_extend) + self.foreground_emg = self._add_emg(a.material) + self.tmgen = self._add_tmg((a.background, a.material, (a.radius, a.height, a.lMax_extend))) + self.bspec = self._add_bspec(a.lMax) def _eval_single_omega(self): # feature: single_omega from .constants import eV, hbar @@ -205,7 +349,7 @@ class ArgParser: 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.omegas = [omega_eV * eh for omega_eV in flatten(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)] @@ -225,7 +369,7 @@ class ArgParser: l = len(self.args.basis_vectors) if l != 2: raise ValueError('Two basis vectors must be specified (have %d)' % l) from .qpms_c import lll_reduce - self.direct_basis = lll_reduce(self.args.basis_vector, delta=1.) + self.direct_basis = lll_reduce(self.args.basis_vectors, delta=1.) import numpy as np self.reciprocal_basis1 = np.linalg.inv(self.direct_basis) self.reciprocal_basis2pi = 2 * np.pi * self.reciprocal_basis1 @@ -255,3 +399,66 @@ class ArgParser: a.theta = a.theta * pi2 a.phi = a.phi * pi2 + def _process_multi_particle(self): # feature: multi_particle + a = self.args + self.tmspecs = {} + self.tmgens = {} + self.bspecs = {} + self.positions = {} + pos13, pos23, pos33 = False, False, False # used to + if len(a.position.keys()) == 0: + warnings.warn("No particle position (-p or +p) specified, assuming single particle in the origin / single particle per unit cell!") + a.position[None] = [(0.,0.,0.)] + for poslabel in a.position.keys(): + try: + lMax = a.lMax.get(poslabel, False) or a.lMax[None] + radius = a.radius.get(poslabel, False) or a.radius[None] + # Height is "inherited" only together with radius + height = a.height.get(poslabel, None) if poslabel in a.radius.keys() else a.height.get(None, None) + if hasattr(a, 'lMax_extend'): + lMax_extend = a.lMax_extend.get(poslabel, False) or a.lMax_extend.get(None, False) or None + else: + lMax_extend = None + material = a.material.get(poslabel, False) or a.material[None] + except (TypeError, KeyError) as exc: + if poslabel is None: + raise ArgumentProcessingError("Unlabeled particles' positions (-p) specified, but some default particle properties are missing (--lMax, --radius, and --material have to be specified)") from exc + else: + raise ArgumentProcessingError(("Incomplete specification of '%s'-labeled particles: you must" + "provide at least ++lMax, ++radius, ++material arguments with the label, or the fallback arguments" + "--lMax, --radius, --material.")%(str(poslabel),)) from exc + tmspec = (a.background, material, (radius, height, lMax_extend)) + self.tmspecs[poslabel] = tmspec + self.tmgens[poslabel] = self._add_tmg(tmspec) + self.bspecs[poslabel] = self._add_bspec(lMax) + poslist_cured = [] + for pos in a.position[poslabel]: + if len(pos) == 1: + pos_cured = (0., 0., pos[0]) + pos13 = True + elif len(pos) == 2: + pos_cured = (pos[0], pos[1], 0.) + pos23 = True + elif len(pos) == 3: + pos_cured = pos + pos33 = True + else: + raise argparse.ArgumentTypeError("Each -p / +p argument requires 1 to 3 cartesian coordinates") + poslist_cured.append(pos_cured) + self.positions[poslabel] = poslist_cured + if pos13 and pos23: + warnings.warn("Both 1D and 2D position specifications used. The former are interpreted as z coordinates while the latter as x, y coordinates") + + def get_particles(self): + """Creates a list of Particle instances that can be directly used in ScatteringSystem.create(). + + Assumes that self._process_multi_particle() has been already called. + """ + from .qpms_c import Particle + plist = [] + for poslabel, poss in self.positions.items(): + t = self.tmgens[poslabel] + bspec = self.bspecs[poslabel] + plist.extend([Particle(pos, t, bspec=bspec) for pos in poss]) + return plist + diff --git a/qpms/qpms_c.pyx b/qpms/qpms_c.pyx index 562e2e3..311e925 100644 --- a/qpms/qpms_c.pyx +++ b/qpms/qpms_c.pyx @@ -726,14 +726,14 @@ cdef class ScatteringSystem: qpms_scatsys_periodic_build_translation_matrix_full(&target_view[0][0], self.s, wavenumber, &blochvector_c) return target - def translation_matrix_packed(self, double k, qpms_iri_t iri, J = QPMS_HANKEL_PLUS): + def translation_matrix_packed(self, cdouble wavenumber, qpms_iri_t iri, J = QPMS_HANKEL_PLUS): self.check_s() cdef size_t rlen = self.saecv_sizes[iri] cdef np.ndarray[np.complex_t, ndim=2] target = np.empty( (rlen,rlen),dtype=complex, order='C') cdef cdouble[:,::1] target_view = target qpms_scatsys_build_translation_matrix_e_irrep_packed(&target_view[0][0], - self.s, iri, k, J) + self.s, iri, wavenumber, J) return target property fullvec_psizes: @@ -1020,6 +1020,9 @@ cdef class _ScatteringSystemAtOmega: def translation_matrix_full(self, blochvector = None): return self.ss_pyref.translation_matrix_full(wavenumber=self.wavenumber, blochvector=blochvector) + def translation_matrix_packed(self, iri, J = QPMS_HANKEL_PLUS): + return self.ss_pyref.translation_matrix_packed(wavenumber=self.wavenumber, iri=iri, J=J) + def scattered_E(self, scatcoeffvector_full, evalpos, bint alt=False, btyp=QPMS_HANKEL_PLUS): cdef qpms_bessel_t btyp_c = BesselType(btyp) evalpos = np.array(evalpos, dtype=float, copy=False)