New CLI argument processing
Former-commit-id: d8fba975ccf08a11e0a4515e5af92edb7856f643
This commit is contained in:
Marek Nečada
parent
1dcebe4fee
commit
f1f2c821df
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@ -1,45 +1,34 @@
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#!/usr/bin/env python3
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import argparse
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import math
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from qpms.argproc import ArgParser
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ap = argparse.ArgumentParser()
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ap = ArgParser(['single_particle', 'single_omega', 'single_lMax'])
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ap.add_argument("-p", "--period", type=float, required=True, help='square lattice period')
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ap.add_argument("--Nx", type=int, required=True, help='Array size x')
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ap.add_argument("--Ny", type=int, required=True, help='Array size y')
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ap.add_argument("-f", "--eV", type=float, required=True, help='radiation angular frequency in eV')
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ap.add_argument("-m", "--material", help='particle material (Au, Ag for Lorentz-Drue or number for constant refractive index)', default='Au', required=True)
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ap.add_argument("-r", "--radius", type=float, required=True, help='particle radius (sphere or cylinder)')
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ap.add_argument("-H", "--height", type=float, help='cylindrical particle height; if not provided, particle is assumed to be spherical')
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ap.add_argument("-k", '--kx-lim', nargs=2, type=float, required=True, help='k vector', metavar=('KX_MIN', 'KX_MAX'))
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# 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)")
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ap.add_argument("--rank-tol", type=float, required=False)
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ap.add_argument("-n", "--refractive-index", type=float, default=1.52, help='background medium refractive index')
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ap.add_argument("-L", "--lMax", type=int, required=True, default=3, help='multipole degree cutoff')
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ap.add_argument("--lMax-extend", type=int, required=False, default=6, help='multipole degree cutoff for T-matrix calculation (cylindrical particles only')
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ap.add_argument("-o", "--output", type=str, required=False, help='output path (if not provided, will be generated automatically)')
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ap.add_argument("-N", type=int, default="151", help="Number of angles")
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ap.add_argument("-O", "--plot-out", type=str, required=False, help="path to plot output (optional)")
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ap.add_argument("-P", "--plot", action='store_true', help="if -p not given, plot to a default path")
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ap.add_argument("-g", "--save-gradually", action='store_true', help="saves the partial result after computing each irrep")
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a=ap.parse_args()
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if a.material in ['Ag', 'Au']:
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pass
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else:
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try: lemat = float(a.material)
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except ValueError:
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try: lemat = complex(a.material)
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except ValueError:
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raise ValueError("--material must be either one of 'Ag', 'Au' or a number")
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a.material = lemat
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import logging
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logging.basicConfig(format='%(asctime)s %(message)s', level=logging.INFO)
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particlestr = ("sph" if a.height is None else "cyl") + ("_r%gnm" % (a.radius*1e9))
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if a.height is not None: particlestr += "_h%gnm" % (a.height * 1e6)
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if a.height is not None: particlestr += "_h%gnm" % (a.height * 1e9)
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defaultprefix = "%s_p%gnm_%dx%d_m%s_n%g_angles(%g_%g)_Ey_f%geV_L%d_cn%d" % (
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particlestr, a.period*1e9, a.Nx, a.Ny, str(a.material), a.refractive_index, a.kx_lim[0], a.kx_lim[1], a.eV, a.lMax, a.N)
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print("Dafault file prefix: %s" % defaultprefix, flush=True)
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logging.info("Dafault file prefix: %s" % defaultprefix)
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import numpy as np
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@ -64,28 +53,17 @@ orig_y = (np.arange(a.Ny/2) + (0 if (a.Ny % 2) else .5)) * py
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orig_xy = np.stack(np.meshgrid(orig_x, orig_y), axis = -1)
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medium = EpsMu(a.refractive_index**2)
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if a.material in lorentz_drude:
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emg = EpsMuGenerator(lorentz_drude[a.material])
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else: # constant refractive index
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emg = EpsMuGenerator(EpsMu(a.material**2))
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if a.height is None:
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tmgen = TMatrixGenerator.sphere(medium, emg, a.radius)
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else:
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tmgen = TMatrixGenerator.cylinder(medium, emg, a.radius, a.height, lMax_extend=a.lMax_extend)
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omega = a.eV * eh
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omega = ap.omega
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bspec = BaseSpec(lMax = a.lMax)
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Tmatrix = tmgen(bspec, omega)
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Tmatrix = ap.tmgen(bspec, ap.omega)
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particles= [Particle(orig_xy[i], Tmatrix) for i in np.ndindex(orig_xy.shape[:-1])]
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sym = FinitePointGroup(point_group_info['D2h'])
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ss = ScatteringSystem(particles, sym)
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wavenumber = medium.k(omega).real # Currently, ScatteringSystem does not "remember" frequency nor wavenumber
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wavenumber = ap.background_epsmu.k(omega).real # Currently, ScatteringSystem does not "remember" frequency nor wavenumber
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sinalpha_list = np.linspace(a.kx_lim[0],a.kx_lim[1],a.N)
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@ -101,9 +79,16 @@ k_cart_list *= wavenumber
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σ_ext_list_ir = np.empty((a.N, ss.nirreps), dtype=float)
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σ_scat_list_ir = np.empty((a.N, ss.nirreps), dtype=float)
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outfile_tmp = defaultprefix + ".tmp" if a.output is None else a.output + ".tmp"
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for iri in range(ss.nirreps):
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logging.info("processing irrep %d/%d" % (iri, ss.nirreps))
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LU = None # to trigger garbage collection before the next call
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translation_matrix = None
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LU = ss.scatter_solver(wavenumber,iri)
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logging.info("LU solver created")
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translation_matrix = ss.translation_matrix_packed(wavenumber, iri, BesselType.REGULAR) + np.eye(ss.saecv_sizes[iri])
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logging.info("auxillary translation matrix created")
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for j in range(a.N):
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# the following two could be calculated only once, but probably not a big deal
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@ -115,6 +100,11 @@ for iri in range(ss.nirreps):
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fi = LU(Tãi)
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σ_ext_list_ir[j, iri] = -np.vdot(ãi, fi).real/wavenumber**2
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σ_scat_list_ir[j, iri] = np.vdot(fi,np.dot(translation_matrix, fi)).real/wavenumber**2
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if a.save_gradually:
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iriout = outfile_tmp + ".%d" % iri
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np.savez(iriout, iri=iri, meta=vars(a), sinalpha=sinalpha_list, k_cart = k_cart_list, E_cart=E_cart_list,
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omega=omega, wavenumber=wavenumber, σ_ext_list_ir=σ_ext_list_ir[:,iri], σ_scat_list_ir=σ_scat_list_ir[:,iri])
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logging.info("partial results saved to %s"%iriout)
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σ_abs_list_ir = σ_ext_list_ir - σ_scat_list_ir
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σ_abs= np.sum(σ_abs_list_ir, axis=-1)
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@ -123,14 +113,17 @@ for iri in range(ss.nirreps):
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outfile = defaultprefix + ".npz" if a.output is None else a.output
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np.savez(outfile, meta=vars(a), k_cart = k_cart_list, E_cart=E_cart_list, σ_ext=σ_ext,σ_abs=σ_abs,σ_scat=σ_scat,
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np.savez(outfile, meta=vars(a), sinalpha=sinalpha_list, k_cart = k_cart_list, E_cart=E_cart_list, σ_ext=σ_ext,σ_abs=σ_abs,σ_scat=σ_scat,
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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
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)
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print("Saved to %s" % outfile)
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logging.info("Saved to %s" % outfile)
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if a.plot or (a.plot_out is not None):
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import matplotlib
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matplotlib.use('pdf')
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from matplotlib import pyplot as plt
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fig = plt.figure()
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ax = fig.add_subplot(111)
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ax.plot(sinalpha_list, σ_ext*1e12,label='$\sigma_\mathrm{ext}$')
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@ -0,0 +1,102 @@
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'''
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Common snippets for argument processing in command line scripts; legacy scripts use scripts_common.py instead.
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'''
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import argparse
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class ArgParser:
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''' Common argument parsing engine for QPMS python CLI scripts. '''
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atomic_arguments = {
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'sqlat_period': lambda ap: ap.add_argument("-p", "--period", type=float, required=True, help='square lattice period'),
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'rectlat_Nx': lambda ap: ap.add_argument("--Nx", type=int, required=True, help='array size x'),
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'rectlat_Ny': lambda ap: ap.add_argument("--Ny", type=int, required=True, help='array size y'),
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'single_frequency_eV': lambda ap: ap.add_argument("-f", "--eV", type=float, required=True, help='radiation angular frequency in eV'),
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'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),
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'single_radius': lambda ap: ap.add_argument("-r", "--radius", type=float, required=True, help='particle radius (sphere or cylinder)'),
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'single_height': lambda ap: ap.add_argument("-H", "--height", type=float, help='cylindrical particle height; if not provided, particle is assumed to be spherical'),
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'single_kvec2': lambda ap: ap.add_argument("-k", '--kx-lim', nargs=2, type=float, required=True, help='k vector', metavar=('KX_MIN', 'KX_MAX')),
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'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)"),
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'bg_refractive_index': lambda ap: ap.add_argument("-n", "--refractive-index", type=float, default=1.52, help='background medium refractive index'),
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'single_lMax': lambda ap: ap.add_argument("-L", "--lMax", type=int, required=True, default=3, help='multipole degree cutoff'),
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'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'),
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'outfile': lambda ap: ap.add_argument("-o", "--output", type=str, required=False, help='output path (if not provided, will be generated automatically)'),
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'plot_out': lambda ap: ap.add_argument("-O", "--plot-out", type=str, required=False, help="path to plot output (optional)"),
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'plot_do': lambda ap: ap.add_argument("-P", "--plot", action='store_true', help="if -p not given, plot to a default path"),
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}
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feature_sets_available = { # name : (description, dependencies, atoms not in other dependencies, methods called after parsing)
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'background': ("Background medium definition (currently only constant epsilon supported)", (), ('bg_refractive_index',), ('_eval_background_epsmu',)),
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'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',)),
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'single_lMax': ("Single particle lMax definition", (), ('single_lMax',), ()),
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'single_omega': ("Single angular frequency", (), ('single_frequency_eV',), ('_eval_single_omega',)),
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}
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def __init__(self, features=[]):
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self.ap = argparse.ArgumentParser()
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self.features_enabled = set()
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self.call_at_parse_list = []
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self.parsed = False
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for feat in features:
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self.add_feature(feat)
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def add_feature(self, feat):
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if feat not in self.features_enabled:
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if feat not in ArgParser.feature_sets_available:
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raise ValueError("Unknown ArgParser feature: %s", feat)
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#resolve dependencies
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_, deps, atoms, atparse = ArgParser.feature_sets_available[feat]
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for dep in deps:
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self.add_feature(dep)
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for atom in atoms: # maybe check whether that atom has already been added sometimes in the future?
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ArgParser.atomic_arguments[atom](self.ap)
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for methodname in atparse:
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self.call_at_parse_list.append(methodname)
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self.features_enabled.add(feat)
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def add_argument(self, *args, **kwargs):
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'''Add a custom argument directly to the standard library ArgParser object'''
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self.ap.add_argument(*args, **kwargs)
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def parse_args(self, process_data = True, *args, **kwargs):
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self.args = self.ap.parse_args(*args, **kwargs)
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if process_data:
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for method in self.call_at_parse_list:
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getattr(self, method)()
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return self.args
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def __getattr__(self, name):
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return getattr(self.args, name)
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# Methods to initialise the related data structures:
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def _eval_background_epsmu(self): # feature: background
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from .cymaterials import EpsMu
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self.background_epsmu = EpsMu(self.args.refractive_index**2)
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def _eval_single_tmgen(self): # feature: single_particle
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a = self.args
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from .cymaterials import EpsMuGenerator, lorentz_drude
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from .cytmatrices import TMatrixGenerator
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if a.material in lorentz_drude.keys():
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self.foreground_emg = EpsMuGenerator(lorentz_drude[a.material])
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else:
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try: lemat = float(a.material)
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except ValueError:
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try: lemat = complex(a.material)
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except ValueError as ve:
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raise ValueError("--material must be either a label such as 'Ag', 'Au', or a number") from ve
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a.material = lemat
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self.foreground_emg = EpsMuGenerator(EpsMu(a.material**2))
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if a.height is None:
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self.tmgen = TMatrixGenerator.sphere(self.background_epsmu, self.foreground_emg, a.radius)
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else:
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self.tmgen = TMatrixGenerator.cylinder(self.background_epsmu, self.foreground_emg, a.radius, a.height, lMax_extend = a.lMax_extend)
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def _eval_single_omega(self): # feature: single_omega
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from .constants import eV, hbar
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self.omega = self.args.eV * eV / hbar
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@ -1,6 +1,6 @@
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# unit conversions, mostly for standalone usage
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# TODO avoid importing the "heavy" qpms parts
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from scipy.constants import epsilon_0 as ε_0, c, pi as π, e as eV, hbar as ℏ, mu_0 as μ_0
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from scipy.constants import epsilon_0 as ε_0, c, pi as π, e as eV, hbar, hbar as ℏ, mu_0 as μ_0
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pi = π
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μm = 1e-6
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nm = 1e-9
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@ -1,3 +1,6 @@
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'''
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Mostly legacy code; new scripts use mostly argproc.py
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'''
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import warnings
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import argparse
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#import sys # for debugging purpose, TODO remove in production
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