More general script for 2D lattice modes.

Former-commit-id: 9b734deabc1b010276fe75e59def698c7eb94b65

examples/hexagonal/modes/00_params.sh

@@ -0,0 +1,33 @@
+#!/bin/bash
+echo 'scale=20;pi=3.14159265358979323846;' > bc_env
+export BC_ENV_ARGS="bc_env"
+
+# We put those into bc, which does not understant exponential notation
+SEPARATION_nm=576
+
+# Particle positions within unit cell
+export P1X_nm=0
+export P1Y_nm=$(bc <<< ${SEPARATION_nm}/2)
+export P2X_nm=0
+export P2Y_nm=-$P1Y_nm
+
+# Lattice vectors
+export A1X_nm=$(bc <<< ${SEPARATION_nm}'*sqrt(3)')
+export A1Y_nm=0
+export A2X_nm=$(bc <<< ${SEPARATION_nm}'*sqrt(3)/2')
+export A2Y_nm=$(bc <<< ${SEPARATION_nm}'*3/2')
+
+# Reciprocal lattice vectors
+export B1X_nmi=$(bc <<< '2*pi/sqrt(3)/'${SEPARATION_nm})
+export B1Y_nmi=$(bc <<< '-2*pi/3/'${SEPARATION_nm})
+export B2X_nmi=0
+export B2Y_nmi=$(bc <<< '4*pi/3/'${SEPARATION_nm})
+
+# a K-point coordinates
+export KPOINTX_nmi=$(bc <<< '4*pi/3/sqrt(3)'/${SEPARATION_nm})
+export KPOINTY_nmi=$(bc <<< '4*pi/3/sqrt(3)'/${SEPARATION_nm})
+
+export RADIUS_nm=50
+export HEIGHT_nm=50
+export METAL=Au
+export BG_REFINDEX=1.52

misc/lat2d_modes.py

@@ -0,0 +1,157 @@
+#!/usr/bin/env python3
+
+import math
+from qpms.argproc import ArgParser, sfloat
+
+ap = ArgParser(['const_real_background', 'lattice2d', 'multi_particle']) # TODO general analytical background
+    
+ap.add_argument("-k", nargs=2, type=sfloat, 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)
+ap.add_argument("-o", "--output", type=str, required=False, help='output path (if not provided, will be generated automatically)')
+ap.add_argument("-t", "--rank-tolerance", type=float, default=1e11)
+ap.add_argument("-c", "--min-candidates", type=int, default=1, help='always try at least this many eigenvalue candidates, even if their SVs in the rank tests are lower than rank_tolerance')
+ap.add_argument("-T", "--residual-tolerance", type=float, default=2.)
+ap.add_argument("-N", type=int, default="150", help="Integration contour discretisation size")
+
+
+#TODO alternative specification of the contour by center and half-axes
+dospec = ap.add_argument_group("Eigenvalue search area by diffracted order specification", "Specification of eigenvalue search area by diffracted order number (requires constant real refractive index for background): the integration contour 'touches' the empty lattice band specified by -b, and its axis lying on the real axis reaches '-f'-way to the next diffractive order")
+dospec.add_argument("-d", "--band-index", type=int, help="Argument's absolute value determines the empty lattice band order (counted from 1), -/+ determines whether the eigenvalues are searched below/above that empty lattice band.", required=True)
+dospec.add_argument("-f", "--interval-factor", type=float, default=0.1, help="Relative length of the integration ellipse axis w.r.t. the interval between two empty lattice bands; this should be be less than 1.") #TODO check
+dospec.add_argument("-i", "--imaginary-aspect-ratio", type=float, default=1., help="Aspect ratio of the integration ellipse (Im/Re); this should not exceed 1/interval_factor.")
+
+ap.add_argument("-P", "--plot", action='store_true', help="if -p not given, plot to a default path")
+ap.add_argument("-O", "--plot-out", type=str, required=False, help="path to plot output (optional)")
+
+a = ap.parse_args()
+
+a1 = ap.direct_basis[0]
+a2 = ap.direct_basis[1]
+
+particlestr = "modes" # TODO particle string specifier or some hash, do this in argproc.py
+defaultprefix = "%s_basis%gnm_%gnm__%gnm_%gnm_n%g_b%+d_k(%g_%g)um-1_cn%d" % (
+            particlestr, a1[0]*1e9, a1[1]*1e9, a2[0]*1e9, a2[1]*1e9, a.refractive_index, a.band_index, a.k[0]*1e-6, a.k[1]*1e-6, a.N)
+
+
+import logging
+logging.basicConfig(format='%(asctime)s %(message)s', level=logging.INFO)
+
+import numpy as np
+import qpms
+from qpms.cybspec import BaseSpec
+from qpms.cytmatrices import CTMatrix
+from qpms.qpms_c import Particle, ScatteringSystem, empty_lattice_modes_xy
+from qpms.cymaterials import EpsMu, EpsMuGenerator, LorentzDrudeModel, lorentz_drude
+from qpms.constants import eV, hbar
+eh = eV/hbar
+
+def inside_ellipse(point_xy, centre_xy, halfaxes_xy):
+    x = point_xy[0] - centre_xy[0]
+    y = point_xy[1] - centre_xy[1]
+    ax = halfaxes_xy[0]
+    ay = halfaxes_xy[1]
+    return ((x/ax)**2 + (y/ay)**2) <= 1
+
+beta = np.array(a.k)
+
+if True: # TODO alternative specification of the contour by center and half-axes
+    empty_freqs = empty_lattice_modes_xy(ap.background_epsmu, ap.reciprocal_basis2pi, np.array([0,0]), 1)
+    empty_freqs = empty_lattice_modes_xy(ap.background_epsmu, ap.reciprocal_basis2pi, beta, (1+abs(a.band_index)) * empty_freqs[1])
+
+    # make the frequencies in the list unique
+    empty_freqs = list(empty_freqs)
+    i = 0
+    while i < len(empty_freqs) - 1:
+        if math.isclose(empty_freqs[i], empty_freqs[i+1], rel_tol=1e-13):
+            del empty_freqs[i+1]
+        else:
+            i += 1
+
+    logging.info("Empty freqs: %s", str(empty_freqs))
+    logging.info("Empty freqs (eV): %s", str([ff / eh for ff in empty_freqs]))
+    if a.band_index > 0:
+        top = empty_freqs[a.band_index]
+        bottom = empty_freqs[a.band_index - 1]
+        lebeta_om = bottom
+    else: # a.band_index < 0
+        top = empty_freqs[abs(a.band_index) - 1]
+        bottom = empty_freqs[abs(a.band_index) - 2] if abs(a.band_index) > 1 else 0.
+        lebeta_om = top
+    #print(top,bottom,lebeta_om)
+    freqradius = .5 * (top - bottom) * a.interval_factor
+
+    centfreq = bottom + freqradius if a.band_index > 0 else top - freqradius
+    if freqradius == 0:
+            raise ValueError("Integration contour radius is set to zero. Are you trying to look below the lowest empty lattice band at the gamma point?")
+
+    freqradius *= (1-1e-13) # to not totally touch the singularities
+
+logging.info("Direct lattice basis: %s" % str(ap.direct_basis))
+logging.info("Reciprocal lattice basis: %s" % str(ap.reciprocal_basis2pi))
+
+ss, ssw = ScatteringSystem.create(ap.get_particles(), ap.background_emg, centfreq, latticebasis=ap.direct_basis)
+
+logging.info("Finding eigenvalues around %s (= %s eV)" % (str(centfreq), str(centfreq/eh)))
+logging.info("Real half-axis %s (= %s eV)" % (str(freqradius), str(freqradius/eh)))
+logging.info("Imaginary half-axis %s (= %s eV)" % (str(freqradius*a.imaginary_aspect_ratio), str(freqradius*a.imaginary_aspect_ratio/eh)))
+
+with qpms.pgsl_ignore_error(15):
+    res = ss.find_modes(centfreq, freqradius, freqradius * a.imaginary_aspect_ratio,
+            blochvector = a.k, contour_points = a.N, rank_tol = a.rank_tolerance,
+            res_tol = a.residual_tolerance, rank_min_sel = a.min_candidates)
+
+logging.info("Eigenfrequencies found: %s" % str(res['eigval']))
+logging.info("Eigenfrequencies found (eV): %s" % str(res['eigval'] / eh))
+
+res['inside_contour'] = inside_ellipse((res['eigval'].real, res['eigval'].imag),
+         (centfreq.real, centfreq.imag), (freqradius, freqradius * a.imaginary_aspect_ratio))
+
+#res['refractive_index_internal'] = [emg(om).n for om in res['eigval']]
+
+#del res['omega']  If contour points are not needed...
+#del res['ImTW'] # not if dbg=false anyway
+outfile = defaultprefix + ".npz" if a.output is None else a.output
+np.savez(outfile, meta=vars(a), empty_freqs=np.array(empty_freqs), **res)
+logging.info("Saved to %s" % outfile)
+
+
+if a.plot or (a.plot_out is not None):
+    if len(res['eigval']) == 0:
+        logging.info("No eigenvalues found; nothing to plot")
+        exit(1)
+    imcut = np.linspace(0, -freqradius)
+    recut1 = np.sqrt(lebeta_om**2+imcut**2) # incomplete Gamma-related cut
+    recut2 = np.sqrt((lebeta_om/2)**2-imcut**2) + lebeta_om/2 # odd-power-lilgamma-related cut
+
+    import matplotlib
+    matplotlib.use('pdf')
+    from matplotlib import pyplot as plt
+
+    fig = plt.figure()
+    ax = fig.add_subplot(111,)
+    #ax.plot(res['omega'].real/eh, res['omega'].imag/eh*1e3, ':') #res['omega'] not implemented in ScatteringSystem
+    ax.add_artist(matplotlib.patches.Ellipse((centfreq.real/eh, centfreq.imag/eh*1e3),
+        2*freqradius/eh, 2*freqradius*a.imaginary_aspect_ratio/eh*1e3, fill=False,
+        ls=':'))
+    ax.scatter(x=res['eigval'].real/eh, y=res['eigval'].imag/eh*1e3 , c = res['inside_contour']
+                      )
+    ax.plot(recut1/eh, imcut/eh*1e3)
+    ax.plot(recut2/eh, imcut/eh*1e3)
+    for i,om in enumerate(res['eigval']):
+            ax.annotate(str(i), (om.real/eh, om.imag/eh*1e3))
+    xmin = np.amin(res['eigval'].real)/eh
+    xmax = np.amax(res['eigval'].real)/eh
+    xspan = xmax-xmin
+    ymin = np.amin(res['eigval'].imag)/eh*1e3
+    ymax = np.amax(res['eigval'].imag)/eh*1e3
+    yspan = ymax-ymin
+    ax.set_xlim([xmin-.1*xspan, xmax+.1*xspan])
+    ax.set_ylim([ymin-.1*yspan, ymax+.1*yspan])
+    ax.set_xlabel('$\hbar \Re \omega / \mathrm{eV}$')
+    ax.set_ylabel('$\hbar \Im \omega / \mathrm{meV}$')
+    plotfile = defaultprefix + ".pdf" if a.plot_out is None else a.plot_out
+    fig.savefig(plotfile)
+
+exit(0)
+

qpms/argproc.py

@@ -100,6 +100,20 @@ def float_range(string):
         else:
             return np.arange(first, last, increment)
 
+def sfloat(string):
+    '''Tries to match a float, or a float with prepended 's'
+
+    Used as a workaraound for argparse's negative number matcher, which does not recognize
+    scientific notation.
+    '''
+    try:
+        res = float(string)
+    except ValueError as exc:
+        if string[0] == 's':
+            res = float(string[1:])
+        else: raise exc
+    return res
+
 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.
@@ -146,9 +160,9 @@ class ArgParser:
 
     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',
+        mpgrp.add_argument("-p", "--position", nargs='+', action=make_dict_action(argtype=sfloat, 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', 
+        mpgrp.add_argument("+p", "++position", nargs='+', action=make_dict_action(argtype=sfloat, 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,),
@@ -185,7 +199,7 @@ class ArgParser:
             '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')),
+            'single_kvec2': lambda ap: ap.add_argument("-k", '--kx-lim', nargs=2, type=sfloat, 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_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)"),
@@ -194,7 +208,7 @@ class ArgParser:
             '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", nargs='+', action=AppendTupleAction, help="basis vector in xy-cartesian coordinates (two required)", required=True, 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, type=sfloat, dest='basis_vectors', metavar=('X', 'Y')),
             'planewave_pol_angles': __add_planewave_argparse_group,
             'multi_particle': __add_manyparticle_argparse_group,
     }
@@ -293,7 +307,11 @@ class ArgParser:
 
     def add_argument(self, *args, **kwargs):
         '''Add a custom argument directly to the standard library ArgParser object'''
-        self.ap.add_argument(*args, **kwargs)
+        return self.ap.add_argument(*args, **kwargs)
+    
+    def add_argument_group(self, *args, **kwargs):
+        '''Add a custom argument group directly to the standard library ArgParser object'''
+        return self.ap.add_argument_group(*args, **kwargs)
 
     def parse_args(self, process_data = True,  *args, **kwargs):
         self.args = self.ap.parse_args(*args, **kwargs)

qpms/cytmatrices.pyx

@@ -211,7 +211,7 @@ cdef class __AxialSymParams:
         self.p.shape = self.shape.g
         if len(args)>0:
             self.lMax_extend = args[0]
-        if 'lMax_extend' in kwargs.keys():
+        if 'lMax_extend' in kwargs.keys() and kwargs['lMax_extend'] is not None:
             self.lMax_extend = kwargs['lMax_extend']
         if self.lMax_extend == 0:
             self.lMax_extend = 1