From 93118cfc07a7ef61c1f9ed5f7bbe9c09d5947455 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marek=20Ne=C4=8Dada?= Date: Thu, 2 Jul 2020 21:59:27 +0300 Subject: [PATCH] [cleanup] Great purge of obsolete scripts Some of the purged scripts might be desirable to reimplement using the new API, especially those related to hexagonal lattices. --- misc/dispersion-SVD.py | 547 -------------------------------- misc/dispersion2D-SVD.py | 403 ----------------------- misc/dispersion_hex_chunks.py | 239 -------------- misc/finitesqlatzsym-scatter.py | 376 ---------------------- misc/generaldisp.py | 340 -------------------- misc/iht-saving.py | 35 -- misc/processWfiles.py | 11 - misc/processWfiles2part.py | 10 - misc/processWfiles_sortnames.py | 13 - misc/riinfo2c.py | 31 -- misc/subroutines-mstm | 85 ----- qpms/argproc.py | 2 +- qpms/modules.rst | 10 - qpms/scripts_common.py | 375 ---------------------- qpms/timetrack.py | 35 -- 15 files changed, 1 insertion(+), 2511 deletions(-) delete mode 100755 misc/dispersion-SVD.py delete mode 100755 misc/dispersion2D-SVD.py delete mode 100755 misc/dispersion_hex_chunks.py delete mode 100755 misc/finitesqlatzsym-scatter.py delete mode 100755 misc/generaldisp.py delete mode 100644 misc/iht-saving.py delete mode 100755 misc/processWfiles.py delete mode 100755 misc/processWfiles2part.py delete mode 100755 misc/processWfiles_sortnames.py delete mode 100644 misc/riinfo2c.py delete mode 100644 misc/subroutines-mstm delete mode 100644 qpms/modules.rst delete mode 100644 qpms/scripts_common.py delete mode 100644 qpms/timetrack.py diff --git a/misc/dispersion-SVD.py b/misc/dispersion-SVD.py deleted file mode 100755 index b3cc64b..0000000 --- a/misc/dispersion-SVD.py +++ /dev/null @@ -1,547 +0,0 @@ -#!/usr/bin/env python3 - - -import argparse, re, random, string -import subprocess -from scipy.constants import hbar, e as eV, pi, c - -def make_action_sharedlist(opname, listname): - class opAction(argparse.Action): - def __call__(self, parser, args, values, option_string=None): - if (not hasattr(args, listname)) or getattr(args, listname) is None: - setattr(args, listname, list()) - getattr(args,listname).append((opname, values)) - return opAction - -parser = argparse.ArgumentParser() -#TODO? použít type=argparse.FileType('r') ? -parser.add_argument('--TMatrix', action='store', required=True, help='Path to TMatrix file') -parser.add_argument('--griddir', action='store', required=True, help='Path to the directory with precalculated translation operators') -#sizepar = parser.add_mutually_exclusive_group(required=True) -parser.add_argument('--hexside', action='store', type=float, required=True, help='Lattice hexagon size length') -parser.add_argument('--output', action='store', help='Path to output PDF') -parser.add_argument('--store_SVD', action='store_true', help='If specified without --SVD_output, it will save the data in a file named as the PDF output, but with .npz extension instead') -#parser.add_argument('--SVD_output', action='store', help='Path to output singular value decomposition result') -parser.add_argument('--nSV', action='store', metavar='N', type=int, default=1, help='Store and draw N minimun singular values') -parser.add_argument('--scp_to', action='store', metavar='N', type=str, help='SCP the output files to a given destination') -parser.add_argument('--background_permittivity', action='store', type=float, default=1., help='Background medium relative permittivity (default 1)') -parser.add_argument('--sparse', action='store', type=int, help='Skip frequencies for preview') -parser.add_argument('--eVmax', action='store', type=float, help='Skip frequencies above this value') -parser.add_argument('--eVmin', action='store', type=float, help='Skip frequencies below this value') -parser.add_argument('--kdensity', action='store', type=int, default=66, help='Number of k-points per x-axis segment') -parser.add_argument('--lMax', action='store', type=int, help='Override lMax from the TMatrix file') -#TODO some more sophisticated x axis definitions -parser.add_argument('--gaussian', action='store', type=float, metavar='σ', help='Use a gaussian envelope for weighting the interaction matrix contributions (depending on the distance), measured in unit cell lengths (?) FIxME).') -popgrp=parser.add_argument_group(title='Operations') -popgrp.add_argument('--tr', dest='ops', action=make_action_sharedlist('tr', 'ops'), default=list()) # the default value for dest can be set once -popgrp.add_argument('--tr0', dest='ops', action=make_action_sharedlist('tr0', 'ops')) -popgrp.add_argument('--tr1', dest='ops', action=make_action_sharedlist('tr1', 'ops')) -popgrp.add_argument('--sym', dest='ops', action=make_action_sharedlist('sym', 'ops')) -popgrp.add_argument('--sym0', dest='ops', action=make_action_sharedlist('sym0', 'ops')) -popgrp.add_argument('--sym1', dest='ops', action=make_action_sharedlist('sym1', 'ops')) -#popgrp.add_argument('--mult', dest='ops', nargs=3, metavar=('INCSPEC', 'SCATSPEC', 'MULTIPLIER'), action=make_action_sharedlist('mult', 'ops')) -#popgrp.add_argument('--mult0', dest='ops', nargs=3, metavar=('INCSPEC', 'SCATSPEC', 'MULTIPLIER'), action=make_action_sharedlist('mult0', 'ops')) -#popgrp.add_argument('--mult1', dest='ops', nargs=3, metavar=('INCSPEC', 'SCATSPEC', 'MULTIPLIER'), action=make_action_sharedlist('mult1', 'ops')) -popgrp.add_argument('--multl', dest='ops', nargs=3, metavar=('INCL[,INCL,...]', 'SCATL[,SCATL,...]', 'MULTIPLIER'), action=make_action_sharedlist('multl', 'ops')) -popgrp.add_argument('--multl0', dest='ops', nargs=3, metavar=('INCL[,INCL,...]', 'SCATL[,SCATL,...]', 'MULTIPLIER'), action=make_action_sharedlist('multl0', 'ops')) -popgrp.add_argument('--multl1', dest='ops', nargs=3, metavar=('INCL[,INCL,...]', 'SCATL[,SCATL,...]', 'MULTIPLIER'), action=make_action_sharedlist('multl1', 'ops')) -parser.add_argument('--frequency_multiplier', action='store', type=float, default=1., help='Multiplies the frequencies in the TMatrix file by a given factor.') -# TODO enable more flexible per-sublattice specification -pargs=parser.parse_args() -print(pargs) - - -translations_dir = pargs.griddir -TMatrix_file = pargs.TMatrix -pdfout = pargs.output if pargs.output else (''.join(random.choice(string.ascii_uppercase + string.digits) for _ in range(10)) + '.pdf') -print(pdfout) -if(pargs.store_SVD): - if re.search('.pdf$', pdfout): - svdout = re.sub('.pdf$', r'.npz', pdfout) - else: - svdout = pdfout + '.npz' -else: - svdout = None - - -hexside = pargs.hexside #375e-9 -epsilon_b = pargs.background_permittivity #2.3104 -gaussianSigma = pargs.gaussian if pargs.gaussian else None # hexside * 222 / 7 -interpfreqfactor = pargs.frequency_multiplier -scp_dest = pargs.scp_to if pargs.scp_to else None -kdensity = pargs.kdensity -minfreq = pargs.eVmin*eV/hbar if pargs.eVmin else None -maxfreq = pargs.eVmax*eV/hbar if pargs.eVmax else None -skipfreq = pargs.sparse if pargs.sparse else None -svn = pargs.nSV - -# TODO multiplier operation definitions and parsing -#factor13inc = 10 -#factor13scat=10 - -ops = list() -opre = re.compile('(tr|sym|copy|multl|mult)(\d*)') -for oparg in pargs.ops: - opm = opre.match(oparg[0]) - if opm: - ops.append(((opm.group(2),) if opm.group(2) else (0,1), opm.group(1), oparg[1])) - else: - raise # should not happen -print(ops) - -#ops = ( -# # co, typ operace (symetrizace / transformace / kopie), specifikace (operace nebo zdroj), -# # co: 0, 1, (0,1), (0,), (1,), #NI: 'all' -# # typ operace: sym, tr, copy -# # specifikace: -# # sym, tr: 'σ_z', 'σ_y', 'C2'; sym: 'C3', -# # copy: 0, 1 (zdroj) -# ((0,1), 'sym', 'σ_z'), -# #((0,1), 'sym', 'σ_x'), -# #((0,1), 'sym', 'σ_y'), -# ((0,1), 'sym', 'C3'), -# ((1), 'tr', 'C2'), -# -#) - -# -----------------finished basic CLI parsing (except for op arguments) ------------------ -import time -begtime=time.time() - -from matplotlib.path import Path -import matplotlib.patches as patches -import matplotlib.pyplot as plt -import qpms -import numpy as np -import os, sys, warnings, math -from matplotlib import pyplot as plt -from matplotlib.backends.backend_pdf import PdfPages -from scipy import interpolate -nx = None -s3 = math.sqrt(3) - - - -pdf = PdfPages(pdfout) - -# In[3]: - -# specifikace T-matice zde -cdn = c/ math.sqrt(epsilon_b) -TMatrices_orig, freqs_orig, freqs_weirdunits_orig, lMaxTM = qpms.loadScuffTMatrices(TMatrix_file) -if pargs.lMax: - lMax = pargs.lMax if pargs.lMax else lMaxTM -my, ny = qpms.get_mn_y(lMax) -nelem = len(my) -if pargs.lMax: #force commandline specified lMax - TMatrices_orig = TMatrices_orig[...,0:nelem,:,0:nelem] - -ž = np.arange(2*nelem) -tž = ž // nelem -mž = my[ž%nelem] -nž = ny[ž%nelem] -TEž = ž[(mž+nž+tž) % 2 == 0] -TMž = ž[(mž+nž+tž) % 2 == 1] - -č = np.arange(2*2*nelem) -žč = č % (2* nelem) -tč = tž[žč] -mč = mž[žč] -nč = nž[žč] -TEč = č[(mč+nč+tč) % 2 == 0] -TMč = č[(mč+nč+tč) % 2 == 1] - -TMatrices = np.array(np.broadcast_to(TMatrices_orig[:,nx,:,:,:,:],(len(freqs_orig),2,2,nelem,2,nelem)) ) - -#TMatrices[:,:,:,:,:,ny==3] *= factor13inc -#TMatrices[:,:,:,ny==3,:,:] *= factor13scat -xfl = qpms.xflip_tyty(lMax) -yfl = qpms.yflip_tyty(lMax) -zfl = qpms.zflip_tyty(lMax) -c2rot = qpms.apply_matrix_left(qpms.yflip_yy(3),qpms.xflip_yy(3),-1) - -reCN = re.compile('(\d*)C(\d+)') -#TODO C nekonečno - -for op in ops: - if op[0] == 'all': - targets = (0,1) - elif isinstance(op[0],int): - targets = (op[0],) - else: - targets = op[0] - - if op[1] == 'sym': - mCN = reCN.match(op[2]) # Fuck van Rossum for not having assignments inside expressions - if op[2] == 'σ_z': - for t in targets: - TMatrices[:,t] = (TMatrices[:,t] + qpms.apply_ndmatrix_left(zfl,qpms.apply_ndmatrix_left(zfl, TMatrices[:,t], (-4,-3)),(-2,-1)))/2 - elif op[2] == 'σ_y': - for t in targets: - TMatrices[:,t] = (TMatrices[:,t] + qpms.apply_ndmatrix_left(yfl,qpms.apply_ndmatrix_left(yfl, TMatrices[:,t], (-4,-3)),(-2,-1)))/2 - elif op[2] == 'σ_x': - for t in targets: - TMatrices[:,t] = (TMatrices[:,t] + qpms.apply_ndmatrix_left(xfl,qpms.apply_ndmatrix_left(xfl, TMatrices[:,t], (-4,-3)),(-2,-1)))/2 - elif op[2] == 'C2': # special case of the latter - for t in targets: - TMatrices[:,t] = (TMatrices[:,t] + qpms.apply_matrix_left(c2rot,qpms.apply_matrix_left(c2rot, TMatrices[:,t], -3),-1))/2 - elif mCN: - rotN = int(mCN.group(2)) - TMatrix_contribs = np.empty((rotN,TMatrices.shape[0],2,nelem,2,nelem), dtype=np.complex_) - for t in targets: - for i in range(rotN): - rotangle = 2*np.pi*i / rotN - rot = qpms.WignerD_yy_fromvector(lMax,np.array([0,0,rotangle])) - rotinv = qpms.WignerD_yy_fromvector(lMax,np.array([0,0,-rotangle])) - TMatrix_contribs[i] = qpms.apply_matrix_left(rot,qpms.apply_matrix_left(rotinv, TMatrices[:,t], -3),-1) - TMatrices[:,t] = np.sum(TMatrix_contribs, axis=0) / rotN - else: - raise - elif op[1] == 'tr': - mCN = reCN.match(op[2]) # Fuck van Rossum for not having assignments inside expressions - if op[2] == 'σ_z': - for t in targets: - TMatrices[:,t] = qpms.apply_ndmatrix_left(zfl,qpms.apply_ndmatrix_left(zfl, TMatrices[:,t], (-4,-3)),(-2,-1)) - elif op[2] == 'σ_y': - for t in targets: - TMatrices[:,t] = qpms.apply_ndmatrix_left(yfl,qpms.apply_ndmatrix_left(yfl, TMatrices[:,t], (-4,-3)),(-2,-1)) - elif op[2] == 'σ_x': - for t in targets: - TMatrices[:,t] = qpms.apply_ndmatrix_left(xfl,qpms.apply_ndmatrix_left(xfl, TMatrices[:,t], (-4,-3)),(-2,-1)) - elif op[2] == 'C2': - for t in targets: - TMatrices[:,t] = qpms.apply_matrix_left(c2rot,qpms.apply_matrix_left(c2rot, TMatrices[:,t], -3),-1) - elif mCN: - rotN = int(mCN.group(2)) - power = int(mCN.group(1)) if mCN.group(1) else 1 - TMatrix_contribs = np.empty((rotN,TMatrices.shape[0],2,nelem,2,nelem), dtype=np.complex_) - for t in targets: - rotangle = 2*np.pi*power/rotN - rot = qpms.WignerD_yy_fromvector(lMax, np.array([0,0,rotangle])) - rotinv = qpms.WignerD_yy_fromvector(lMax, np.array([0,0,-rotangle])) - TMatrices[:,t] = qpms.apply_matrix_left(rot, qpms.apply_matrix_left(rotinv, TMatrices[:,t], -3),-1) - else: - raise - elif op[1] == 'copy': - raise # not implemented - elif op[1] == 'mult': - raise # not implemented - elif op[1] == 'multl': - incy = np.full((nelem,), False, dtype=bool) - for incl in op[2][0].split(','): - l = int(incl) - incy += (l == ny) - scaty = np.full((nelem,), False, dtype=bool) - for scatl in op[2][1].split(','): - l = int(scatl) - scaty += (l == ny) - for t in targets: - TMatrices[np.ix_(np.arange(TMatrices.shape[0]),np.array([t]),np.array([0,1]),scaty,np.array([0,1]),incy)] *= float(op[2][2]) - else: - raise #unknown operation; should not happen - -TMatrices_interp = interpolate.interp1d(freqs_orig*interpfreqfactor, TMatrices, axis=0, kind='linear',fill_value="extrapolate") - - - -# In[4]: - -om = np.linspace(np.min(freqs_orig), np.max(freqs_orig),100) -TMatrix0ip = np.reshape(TMatrices_interp(om)[:,0], (len(om), 2*nelem*2*nelem)) -f, axa = plt.subplots(2, 2, figsize=(15,15)) - -#print(TMatrices.shape) -#plt.plot(om, TMatrices[:,0,0,0,0].imag,'r',om, TMatrices[:,0,0,0,0].real,'r--',om, TMatrices[:,0,2,0,2].imag,'b',om, TMatrices[:,0,2,0,2].real,'b--')) - -ax = axa[0,0] -ax2 = ax.twiny() -ax2.set_xlim([ax.get_xlim()[0]/eV*hbar,ax.get_xlim()[1]/eV*hbar]) -ax.plot( - om, TMatrix0ip[:,:].imag,'-',om, TMatrix0ip[:,:].real,'--', -) -ax = axa[0,1] -ax2 = ax.twiny() -ax2.set_xlim([ax.get_xlim()[0]/eV*hbar,ax.get_xlim()[1]/eV*hbar]) -ax.plot( - om, abs(TMatrix0ip[:,:]),'-' -) -ax.set_yscale('log') - -ax = axa[1,1] -ax2 = ax.twiny() -ax2.set_xlim([ax.get_xlim()[0]/eV*hbar,ax.get_xlim()[1]/eV*hbar]) -ax.plot( - om, np.unwrap(np.angle(TMatrix0ip[:,:]),axis=0),'-' -) - -ax = axa[1,0] -ax.text(0.5,0.5,str(pargs).replace(',',',\n'),horizontalalignment='center',verticalalignment='center',transform=ax.transAxes) -pdf.savefig(f) - - -# In[ ]: - -#kdensity = 66 #defined from cl arguments -bz_0 = np.array((0,0,0.,)) -bz_K1 = np.array((1.,0,0))*4*np.pi/3/hexside/s3 -bz_K2 = np.array((1./2.,s3/2,0))*4*np.pi/3/hexside/s3 -bz_M = np.array((3./4, s3/4,0))*4*np.pi/3/hexside/s3 -k0Mlist = bz_0 + (bz_M-bz_0) * np.linspace(0,1,kdensity)[:,nx] -kMK1list = bz_M + (bz_K1-bz_M) * np.linspace(0,1,kdensity)[:,nx] -kK10list = bz_K1 + (bz_0-bz_K1) * np.linspace(0,1,kdensity)[:,nx] -k0K2list = bz_0 + (bz_K2-bz_0) * np.linspace(0,1,kdensity)[:,nx] -kK2Mlist = bz_K2 + (bz_M-bz_K2) * np.linspace(0,1,kdensity)[:,nx] -B1 = 2* bz_K1 - bz_K2 -B2 = 2* bz_K2 - bz_K1 -klist = np.concatenate((k0Mlist,kMK1list,kK10list,k0K2list,kK2Mlist), axis=0) -kxmaplist = np.concatenate((np.array([0]),np.cumsum(np.linalg.norm(np.diff(klist, axis=0), axis=-1)))) - - -# In[ ]: - -n2id = np.identity(2*nelem) -n2id.shape = (2,nelem,2,nelem) -extlistlist = list() -leftmatrixlistlist = list() -minsvTElistlist=list() -minsvTMlistlist=list() -if svdout: - svUfullTElistlist = list() - svVfullTElistlist = list() - svSfullTElistlist = list() - svUfullTMlistlist = list() - svVfullTMlistlist = list() - svSfullTMlistlist = list() - -nan = float('nan') -omegalist = list() -filecount = 0 -for trfile in os.scandir(translations_dir): - filecount += 1 - if (skipfreq and filecount % skipfreq): - continue - try: - npz = np.load(trfile.path, mmap_mode='r') - k_0 = npz['precalc_params'][()]['k_hexside'] / hexside - omega = k_0 * c / math.sqrt(epsilon_b) - if((minfreq and omega < minfreq) or (maxfreq and omega > maxfreq)): - continue - except: - print ("Unexpected error, trying to continue with another file:", sys.exc_info()[0]) - continue - try: - tdic = qpms.hexlattice_precalc_AB_loadunwrap(trfile.path, return_points=True) - except: - print ("Unexpected error, trying to continue with another file:", sys.exc_info()[0]) - continue - k_0 = tdic['k_hexside'] / hexside - omega = k_0 * c / math.sqrt(epsilon_b) - omegalist.append(omega) - print(filecount, omega/eV*hbar) - sys.stdout.flush() - a_self = tdic['a_self'][:,:nelem,:nelem] - b_self = tdic['b_self'][:,:nelem,:nelem] - a_u2d = tdic['a_u2d'][:,:nelem,:nelem] - b_u2d = tdic['b_u2d'][:,:nelem,:nelem] - a_d2u = tdic['a_d2u'][:,:nelem,:nelem] - b_d2u = tdic['b_d2u'][:,:nelem,:nelem] - unitcell_translations = tdic['self_tr']*hexside*s3 - u2d_translations = tdic['u2d_tr']*hexside*s3 - d2u_translations = tdic['d2u_tr']*hexside*s3 - if gaussianSigma: - unitcell_envelope = np.exp(-np.sum(tdic['self_tr']**2,axis=-1)/(2*gaussianSigma**2)) - u2d_envelope = np.exp(-np.sum(tdic['u2d_tr']**2,axis=-1)/(2*gaussianSigma**2)) - d2u_envelope = np.exp(-np.sum(tdic['d2u_tr']**2,axis=-1)/(2*gaussianSigma**2)) - - - TMatrices_om = TMatrices_interp(omega) - if svdout: - svUfullTElist = np.full((klist.shape[0], 2*nelem, 2*nelem), np.nan, dtype=complex) - svVfullTElist = np.full((klist.shape[0], 2*nelem, 2*nelem), np.nan, dtype=complex) - svSfullTElist = np.full((klist.shape[0], 2*nelem), np.nan, dtype=complex) - svUfullTMlist = np.full((klist.shape[0], 2*nelem, 2*nelem), np.nan, dtype=complex) - svVfullTMlist = np.full((klist.shape[0], 2*nelem, 2*nelem), np.nan, dtype=complex) - svSfullTMlist = np.full((klist.shape[0], 2*nelem), np.nan, dtype=complex) - - - minsvTElist = np.full((klist.shape[0], svn),np.nan) - minsvTMlist = np.full((klist.shape[0], svn),np.nan) - leftmatrixlist = np.full((klist.shape[0],2,2,nelem,2,2,nelem),np.nan,dtype=complex) - isNaNlist = np.zeros((klist.shape[0]), dtype=bool) - - # sem nějaká rozumná smyčka - for ki in range(klist.shape[0]): - k = klist[ki] - if (k_0*k_0 - k[0]*k[0] - k[1]*k[1] < 0): - isNaNlist[ki] = True - continue - - phases_self = np.exp(1j*np.tensordot(k,unitcell_translations,axes=(0,-1))) - phases_u2d = np.exp(1j*np.tensordot(k,u2d_translations,axes=(0,-1))) - phases_d2u = np.exp(1j*np.tensordot(k,d2u_translations,axes=(0,-1))) - if gaussianSigma: - phases_self *= unitcell_envelope - phases_u2d *= u2d_envelope - phases_d2u *= d2u_envelope - leftmatrix = np.zeros((2,2,nelem, 2,2,nelem), dtype=complex) - - leftmatrix[0,0,:,0,0,:] = np.tensordot(a_self,phases_self, axes=(0,-1)) # u2u, E2E - leftmatrix[1,0,:,1,0,:] = leftmatrix[0,0,:,0,0,:] # d2d, E2E - leftmatrix[0,1,:,0,1,:] = leftmatrix[0,0,:,0,0,:] # u2u, M2M - leftmatrix[1,1,:,1,1,:] = leftmatrix[0,0,:,0,0,:] # d2d, M2M - leftmatrix[0,0,:,0,1,:] = np.tensordot(b_self,phases_self, axes=(0,-1)) # u2u, M2E - leftmatrix[0,1,:,0,0,:] = leftmatrix[0,0,:,0,1,:] # u2u, E2M - leftmatrix[1,1,:,1,0,:] = leftmatrix[0,0,:,0,1,:] # d2d, E2M - leftmatrix[1,0,:,1,1,:] = leftmatrix[0,0,:,0,1,:] # d2d, M2E - leftmatrix[0,0,:,1,0,:] = np.tensordot(a_d2u, phases_d2u,axes=(0,-1)) #d2u,E2E - leftmatrix[0,1,:,1,1,:] = leftmatrix[0,0,:,1,0,:] #d2u, M2M - leftmatrix[1,0,:,0,0,:] = np.tensordot(a_u2d, phases_u2d,axes=(0,-1)) #u2d,E2E - leftmatrix[1,1,:,0,1,:] = leftmatrix[1,0,:,0,0,:] #u2d, M2M - leftmatrix[0,0,:,1,1,:] = np.tensordot(b_d2u, phases_d2u,axes=(0,-1)) #d2u,M2E - leftmatrix[0,1,:,1,0,:] = leftmatrix[0,0,:,1,1,:] #d2u, E2M - leftmatrix[1,0,:,0,1,:] = np.tensordot(b_u2d, phases_u2d,axes=(0,-1)) #u2d,M2E - leftmatrix[1,1,:,0,0,:] = leftmatrix[1,0,:,0,1,:] #u2d, E2M - #leftmatrix is now the translation matrix T - for j in range(2): - leftmatrix[j] = -np.tensordot(TMatrices_om[j], leftmatrix[j], axes=([-2,-1],[0,1])) - # at this point, jth row of leftmatrix is that of -MT - leftmatrix[j,:,:,j,:,:] += n2id - #now we are done, 1-MT - - leftmatrixlist[ki] = leftmatrix - - - nnlist = np.logical_not(isNaNlist) - leftmatrixlist_s = np.reshape(leftmatrixlist,(klist.shape[0], 2*2*nelem,2*2*nelem))[nnlist] - leftmatrixlist_TE = leftmatrixlist_s[np.ix_(np.arange(leftmatrixlist_s.shape[0]),TEč,TEč)] - leftmatrixlist_TM = leftmatrixlist_s[np.ix_(np.arange(leftmatrixlist_s.shape[0]),TMč,TMč)] - #svarr = np.linalg.svd(leftmatrixlist_TE, compute_uv=False) - #argsortlist = np.argsort(svarr, axis=-1)[...,:svn] - #minsvTElist[nnlist] = svarr[...,argsortlist] - #minsvTElist[nnlist] = np.amin(np.linalg.svd(leftmatrixlist_TE, compute_uv=False), axis=-1) - if svdout: - svUfullTElist[nnlist], svSfullTElist[nnlist], svVfullTElist[nnlist] = np.linalg.svd(leftmatrixlist_TE, compute_uv=True) - svUfullTMlist[nnlist], svSfullTMlist[nnlist], svVfullTMlist[nnlist] = np.linalg.svd(leftmatrixlist_TM, compute_uv=True) - svUfullTElistlist.append(svUfullTElist) - svVfullTElistlist.append(svVfullTElist) - svSfullTElistlist.append(svSfullTElist) - svUfullTMlistlist.append(svUfullTMlist) - svVfullTMlistlist.append(svVfullTMlist) - svSfullTMlistlist.append(svSfullTMlist) - minsvTElist[nnlist] = np.linalg.svd(leftmatrixlist_TE, compute_uv=False)[...,-svn:] - #svarr = np.linalg.svd(leftmatrixlist_TM, compute_uv=False) - #argsortlist = np.argsort(svarr, axis=-1)[...,:svn] - #minsvTMlist[nnlist] = svarr[...,argsortlist] - #minsvTMlist[nnlist] = np.amin(np.linalg.svd(leftmatrixlist_TM, compute_uv=False), axis=-1) - minsvTMlist[nnlist] = np.linalg.svd(leftmatrixlist_TM, compute_uv=False)[...,-svn:] - minsvTMlistlist.append(minsvTMlist) - minsvTElistlist.append(minsvTElist) - -minsvTElistarr = np.array(minsvTElistlist) -minsvTMlistarr = np.array(minsvTMlistlist) -del minsvTElistlist, minsvTMlistlist -if svdout: - svUfullTElistarr = np.array(svUfullTElistlist) - svVfullTElistarr = np.array(svVfullTElistlist) - svSfullTElistarr = np.array(svSfullTElistlist) - del svUfullTElistlist, svVfullTElistlist, svSfullTElistlist - svUfullTMlistarr = np.array(svUfullTMlistlist) - svVfullTMlistarr = np.array(svVfullTMlistlist) - svSfullTMlistarr = np.array(svSfullTMlistlist) - del svUfullTMlistlist, svVfullTMlistlist, svSfullTMlistlist -omegalist = np.array(omegalist) -# order to make the scatter plots "nice" -omegaorder = np.argsort(omegalist) -omegalist = omegalist[omegaorder] -minsvTElistarr = minsvTElistarr[omegaorder] -minsvTMlistarr = minsvTMlistarr[omegaorder] -if svdout: - svUfullTElistarr = svUfullTElistarr[omegaorder] - svVfullTElistarr = svVfullTElistarr[omegaorder] - svSfullTElistarr = svSfullTElistarr[omegaorder] - svUfullTMlistarr = svUfullTMlistarr[omegaorder] - svVfullTMlistarr = svVfullTMlistarr[omegaorder] - svSfullTMlistarr = svSfullTMlistarr[omegaorder] - np.savez(svdout, omega = omegalist, klist = klist, bzpoints = np.array([bz_0, bz_K1, bz_K2, bz_M, B1, B2]), - uTE = svUfullTElistarr, - vTE = svVfullTElistarr, - sTE = svSfullTElistarr, - uTM = svUfullTMlistarr, - vTM = svVfullTMlistarr, - sTM = svSfullTMlistarr, - ) - - -omlist = np.broadcast_to(omegalist[:,nx], minsvTElistarr[...,0].shape) -kxmlarr = np.broadcast_to(kxmaplist[nx,:], minsvTElistarr[...,0].shape) -klist = np.concatenate((k0Mlist,kMK1list,kK10list,k0K2list,kK2Mlist), axis=0) - - -# In[ ]: -for minN in reversed(range(svn)): - f, ax = plt.subplots(1, figsize=(20,15)) - sc = ax.scatter(kxmlarr, omlist/eV*hbar, c = np.sqrt(minsvTMlistarr[...,minN]), s =40, lw=0) - ax.plot(kxmaplist, np.linalg.norm(klist,axis=-1)*cdn/eV*hbar, '-', - kxmaplist, np.linalg.norm(klist+B1, axis=-1)*cdn/eV*hbar, '-', - kxmaplist, np.linalg.norm(klist+B2, axis=-1)*cdn/eV*hbar, '-', - kxmaplist, np.linalg.norm(klist-B2, axis=-1)*cdn/eV*hbar, '-', - kxmaplist, np.linalg.norm(klist-B1, axis=-1)*cdn/eV*hbar, '-', - kxmaplist, np.linalg.norm(klist+B2-B1, axis=-1)*cdn/eV*hbar, '-', - kxmaplist, np.linalg.norm(klist-B2+B1, axis=-1)*cdn/eV*hbar, '-', - kxmaplist, np.linalg.norm(klist-B2-B1, axis=-1)*cdn/eV*hbar, '-', - kxmaplist, np.linalg.norm(klist+B2+B1, axis=-1)*cdn/eV*hbar, '-', - kxmaplist, np.linalg.norm(klist-2*B1, axis=-1)*cdn/eV*hbar, '-', - kxmaplist, np.linalg.norm(klist-2*B2, axis=-1)*cdn/eV*hbar, '-', - kxmaplist, np.linalg.norm(klist-2*B2-B1, axis=-1)*cdn/eV*hbar, '-', - kxmaplist, np.linalg.norm(klist-2*B1-B2, axis=-1)*cdn/eV*hbar, '-', - kxmaplist, np.linalg.norm(klist-2*B1-2*B2, axis=-1)*cdn/eV*hbar, '-', - # kxmaplist, np.linalg.norm(klist+2*B2-B1, axis=-1)*cdn, '-', - # kxmaplist, np.linalg.norm(klist+2*B1-B2, axis=-1)*cdn, '-', - ) - ax.set_xlim([np.min(kxmlarr),np.max(kxmlarr)]) - #ax.set_ylim([2.15,2.30]) - ax.set_ylim([np.min(omlist/eV*hbar),np.max(omlist/eV*hbar)]) - ax.set_xticks([0, kxmaplist[len(k0Mlist)-1], kxmaplist[len(k0Mlist)+len(kMK1list)-1], kxmaplist[len(k0Mlist)+len(kMK1list)+len(kK10list)-1], kxmaplist[len(k0Mlist)+len(kMK1list)+len(kK10list)+len(k0K2list)-1], kxmaplist[len(k0Mlist)+len(kMK1list)+len(kK10list)+len(k0K2list)+len(kK2Mlist)-1]]) - ax.set_xticklabels(['Γ', 'M', 'K', 'Γ', 'K\'','M']) - f.colorbar(sc) - - pdf.savefig(f) - - - # In[ ]: - - f, ax = plt.subplots(1, figsize=(20,15)) - sc = ax.scatter(kxmlarr, omlist/eV*hbar, c = np.sqrt(minsvTElistarr[...,minN]), s =40, lw=0) - ax.plot(kxmaplist, np.linalg.norm(klist,axis=-1)*cdn/eV*hbar, '-', - kxmaplist, np.linalg.norm(klist+B1, axis=-1)*cdn/eV*hbar, '-', - kxmaplist, np.linalg.norm(klist+B2, axis=-1)*cdn/eV*hbar, '-', - kxmaplist, np.linalg.norm(klist-B2, axis=-1)*cdn/eV*hbar, '-', - kxmaplist, np.linalg.norm(klist-B1, axis=-1)*cdn/eV*hbar, '-', - kxmaplist, np.linalg.norm(klist+B2-B1, axis=-1)*cdn/eV*hbar, '-', - kxmaplist, np.linalg.norm(klist-B2+B1, axis=-1)*cdn/eV*hbar, '-', - kxmaplist, np.linalg.norm(klist-B2-B1, axis=-1)*cdn/eV*hbar, '-', - kxmaplist, np.linalg.norm(klist+B2+B1, axis=-1)*cdn/eV*hbar, '-', - kxmaplist, np.linalg.norm(klist-2*B1, axis=-1)*cdn/eV*hbar, '-', - kxmaplist, np.linalg.norm(klist-2*B2, axis=-1)*cdn/eV*hbar, '-', - kxmaplist, np.linalg.norm(klist-2*B2-B1, axis=-1)*cdn/eV*hbar, '-', - kxmaplist, np.linalg.norm(klist-2*B1-B2, axis=-1)*cdn/eV*hbar, '-', - kxmaplist, np.linalg.norm(klist-2*B1-2*B2, axis=-1)*cdn/eV*hbar, '-', - # kxmaplist, np.linalg.norm(klist+2*B2-B1, axis=-1)*cdn, '-', - # kxmaplist, np.linalg.norm(klist+2*B1-B2, axis=-1)*cdn, '-', - ) - ax.set_xlim([np.min(kxmlarr),np.max(kxmlarr)]) - #ax.set_ylim([2.15,2.30]) - ax.set_ylim([np.min(omlist/eV*hbar),np.max(omlist/eV*hbar)]) - ax.set_xticks([0, kxmaplist[len(k0Mlist)-1], kxmaplist[len(k0Mlist)+len(kMK1list)-1], kxmaplist[len(k0Mlist)+len(kMK1list)+len(kK10list)-1], kxmaplist[len(k0Mlist)+len(kMK1list)+len(kK10list)+len(k0K2list)-1], kxmaplist[len(k0Mlist)+len(kMK1list)+len(kK10list)+len(k0K2list)+len(kK2Mlist)-1]]) - ax.set_xticklabels(['Γ', 'M', 'K', 'Γ', 'K\'','M']) - f.colorbar(sc) - - pdf.savefig(f) -pdf.close() - -if scp_dest: - subprocess.run(['scp', pdfout, scp_dest]) - if svdout: - subprocess.run(['scp', svdout, scp_dest]) - -print(time.strftime("%H.%M:%S",time.gmtime(time.time()-begtime))) diff --git a/misc/dispersion2D-SVD.py b/misc/dispersion2D-SVD.py deleted file mode 100755 index 8bc93f9..0000000 --- a/misc/dispersion2D-SVD.py +++ /dev/null @@ -1,403 +0,0 @@ -#!/usr/bin/env python3 - - -import argparse, re, random, string -import subprocess -from scipy.constants import hbar, e as eV, pi, c - -def make_action_sharedlist(opname, listname): - class opAction(argparse.Action): - def __call__(self, parser, args, values, option_string=None): - if (not hasattr(args, listname)) or getattr(args, listname) is None: - setattr(args, listname, list()) - getattr(args,listname).append((opname, values)) - return opAction - -parser = argparse.ArgumentParser() -#TODO? použít type=argparse.FileType('r') ? -parser.add_argument('--TMatrix', action='store', required=True, help='Path to TMatrix file') -#parser.add_argument('--griddir', action='store', required=True, help='Path to the directory with precalculated translation operators') -parser.add_argument('--output_prefix', action='store', required=True, help='Prefix to the pdf and/or npz output (will be appended frequency and hexside)') -#sizepar = parser.add_mutually_exclusive_group(required=True) -parser.add_argument('--hexside', action='store', type=float, required=True, help='Lattice hexagon size length') -parser.add_argument('--output', action='store', help='Path to output PDF') -parser.add_argument('--store_SVD', action='store_false', help='If specified without --SVD_output, it will save the data in a file named as the PDF output, but with .npz extension instead') -parser.add_argument('--plot_TMatrix', action='store_true', help='Visualise TMatrix on the first page of the output') -#parser.add_argument('--SVD_output', action='store', help='Path to output singular value decomposition result') -parser.add_argument('--nSV', action='store', metavar='N', type=int, default=1, help='Store and draw N minimun singular values') -parser.add_argument('--maxlayer', action='store', type=int, default=100, help='How far to sum the lattice points to obtain the dispersion') -parser.add_argument('--scp_to', action='store', metavar='N', type=str, help='SCP the output files to a given destination') -parser.add_argument('--background_permittivity', action='store', type=float, default=1., help='Background medium relative permittivity (default 1)') -parser.add_argument('--eVfreq', action='store', required=True, type=float, help='Frequency in eV') -parser.add_argument('--kdensity', action='store', type=int, default=33, help='Number of k-points per x-axis segment') -parser.add_argument('--lMax', action='store', type=int, help='Override lMax from the TMatrix file') -#TODO some more sophisticated x axis definitions -parser.add_argument('--gaussian', action='store', type=float, metavar='σ', help='Use a gaussian envelope for weighting the interaction matrix contributions (depending on the distance), measured in unit cell lengths (?) FIxME).') -popgrp=parser.add_argument_group(title='Operations') -popgrp.add_argument('--tr', dest='ops', action=make_action_sharedlist('tr', 'ops'), default=list()) # the default value for dest can be set once -popgrp.add_argument('--tr0', dest='ops', action=make_action_sharedlist('tr0', 'ops')) -popgrp.add_argument('--tr1', dest='ops', action=make_action_sharedlist('tr1', 'ops')) -popgrp.add_argument('--sym', dest='ops', action=make_action_sharedlist('sym', 'ops')) -popgrp.add_argument('--sym0', dest='ops', action=make_action_sharedlist('sym0', 'ops')) -popgrp.add_argument('--sym1', dest='ops', action=make_action_sharedlist('sym1', 'ops')) -#popgrp.add_argument('--mult', dest='ops', nargs=3, metavar=('INCSPEC', 'SCATSPEC', 'MULTIPLIER'), action=make_action_sharedlist('mult', 'ops')) -#popgrp.add_argument('--mult0', dest='ops', nargs=3, metavar=('INCSPEC', 'SCATSPEC', 'MULTIPLIER'), action=make_action_sharedlist('mult0', 'ops')) -#popgrp.add_argument('--mult1', dest='ops', nargs=3, metavar=('INCSPEC', 'SCATSPEC', 'MULTIPLIER'), action=make_action_sharedlist('mult1', 'ops')) -popgrp.add_argument('--multl', dest='ops', nargs=3, metavar=('INCL[,INCL,...]', 'SCATL[,SCATL,...]', 'MULTIPLIER'), action=make_action_sharedlist('multl', 'ops')) -popgrp.add_argument('--multl0', dest='ops', nargs=3, metavar=('INCL[,INCL,...]', 'SCATL[,SCATL,...]', 'MULTIPLIER'), action=make_action_sharedlist('multl0', 'ops')) -popgrp.add_argument('--multl1', dest='ops', nargs=3, metavar=('INCL[,INCL,...]', 'SCATL[,SCATL,...]', 'MULTIPLIER'), action=make_action_sharedlist('multl1', 'ops')) -parser.add_argument('--frequency_multiplier', action='store', type=float, default=1., help='Multiplies the frequencies in the TMatrix file by a given factor.') -# TODO enable more flexible per-sublattice specification -pargs=parser.parse_args() -print(pargs) - -maxlayer=pargs.maxlayer -hexside=pargs.hexside -eVfreq = pargs.eVfreq -freq = eVfreq*eV/hbar - -TMatrix_file = pargs.TMatrix -pdfout = pargs.output if pargs.output else ( - '%s_%dnm_%.4f.pdf' % (pargs.output_prefix,hexside/1e-9,eVfreq) if pargs.output_prefix else - (''.join(random.choice(string.ascii_uppercase + string.digits) for _ in range(10)) + '.pdf')) -print(pdfout) -if(pargs.store_SVD): - if re.search('.pdf$', pdfout): - svdout = re.sub('.pdf$', r'.npz', pdfout) - else: - svdout = pdfout + '.npz' -else: - svdout = None - - -epsilon_b = pargs.background_permittivity #2.3104 -gaussianSigma = pargs.gaussian if pargs.gaussian else None # hexside * 222 / 7 -interpfreqfactor = pargs.frequency_multiplier -scp_dest = pargs.scp_to if pargs.scp_to else None -kdensity = pargs.kdensity -svn = pargs.nSV - -# TODO multiplier operation definitions and parsing -#factor13inc = 10 -#factor13scat=10 - -ops = list() -opre = re.compile('(tr|sym|copy|multl|mult)(\d*)') -for oparg in pargs.ops: - opm = opre.match(oparg[0]) - if opm: - ops.append(((opm.group(2),) if opm.group(2) else (0,1), opm.group(1), oparg[1])) - else: - raise # should not happen -print(ops) - -#ops = ( -# # co, typ operace (symetrizace / transformace / kopie), specifikace (operace nebo zdroj), -# # co: 0, 1, (0,1), (0,), (1,), #NI: 'all' -# # typ operace: sym, tr, copy -# # specifikace: -# # sym, tr: 'σ_z', 'σ_y', 'C2'; sym: 'C3', -# # copy: 0, 1 (zdroj) -# ((0,1), 'sym', 'σ_z'), -# #((0,1), 'sym', 'σ_x'), -# #((0,1), 'sym', 'σ_y'), -# ((0,1), 'sym', 'C3'), -# ((1), 'tr', 'C2'), -# -#) - -# -----------------finished basic CLI parsing (except for op arguments) ------------------ -import time -begtime=time.time() - -from matplotlib.path import Path -import matplotlib.patches as patches -import matplotlib.pyplot as plt -import qpms -import numpy as np -import os, sys, warnings, math -from matplotlib import pyplot as plt -from matplotlib.backends.backend_pdf import PdfPages -from scipy import interpolate -nx = None -s3 = math.sqrt(3) - - - -pdf = PdfPages(pdfout) - -# In[3]: - -# specifikace T-matice zde -cdn = c/ math.sqrt(epsilon_b) -TMatrices_orig, freqs_orig, freqs_weirdunits_orig, lMaxTM = qpms.loadScuffTMatrices(TMatrix_file) -lMax = lMaxTM -if pargs.lMax: - lMax = pargs.lMax if pargs.lMax else lMaxTM -my, ny = qpms.get_mn_y(lMax) -nelem = len(my) -if pargs.lMax: #force commandline specified lMax - TMatrices_orig = TMatrices_orig[...,0:nelem,:,0:nelem] - -TMatrices = np.array(np.broadcast_to(TMatrices_orig[:,nx,:,:,:,:],(len(freqs_orig),2,2,nelem,2,nelem)) ) - -#TMatrices[:,:,:,:,:,ny==3] *= factor13inc -#TMatrices[:,:,:,ny==3,:,:] *= factor13scat -xfl = qpms.xflip_tyty(lMax) -yfl = qpms.yflip_tyty(lMax) -zfl = qpms.zflip_tyty(lMax) -c2rot = qpms.apply_matrix_left(qpms.yflip_yy(3),qpms.xflip_yy(3),-1) - -reCN = re.compile('(\d*)C(\d+)') -#TODO C nekonečno - -for op in ops: - if op[0] == 'all': - targets = (0,1) - elif isinstance(op[0],int): - targets = (op[0],) - else: - targets = op[0] - - if op[1] == 'sym': - mCN = reCN.match(op[2]) # Fuck van Rossum for not having assignments inside expressions - if op[2] == 'σ_z': - for t in targets: - TMatrices[:,t] = (TMatrices[:,t] + qpms.apply_ndmatrix_left(zfl,qpms.apply_ndmatrix_left(zfl, TMatrices[:,t], (-4,-3)),(-2,-1)))/2 - elif op[2] == 'σ_y': - for t in targets: - TMatrices[:,t] = (TMatrices[:,t] + qpms.apply_ndmatrix_left(yfl,qpms.apply_ndmatrix_left(yfl, TMatrices[:,t], (-4,-3)),(-2,-1)))/2 - elif op[2] == 'σ_x': - for t in targets: - TMatrices[:,t] = (TMatrices[:,t] + qpms.apply_ndmatrix_left(xfl,qpms.apply_ndmatrix_left(xfl, TMatrices[:,t], (-4,-3)),(-2,-1)))/2 - elif op[2] == 'C2': # special case of the latter - for t in targets: - TMatrices[:,t] = (TMatrices[:,t] + qpms.apply_matrix_left(c2rot,qpms.apply_matrix_left(c2rot, TMatrices[:,t], -3),-1))/2 - elif mCN: - rotN = int(mCN.group(2)) - TMatrix_contribs = np.empty((rotN,TMatrices.shape[0],2,nelem,2,nelem), dtype=np.complex_) - for t in targets: - for i in range(rotN): - rotangle = 2*np.pi*i / rotN - rot = qpms.WignerD_yy_fromvector(lMax,np.array([0,0,rotangle])) - rotinv = qpms.WignerD_yy_fromvector(lMax,np.array([0,0,-rotangle])) - TMatrix_contribs[i] = qpms.apply_matrix_left(rot,qpms.apply_matrix_left(rotinv, TMatrices[:,t], -3),-1) - TMatrices[:,t] = np.sum(TMatrix_contribs, axis=0) / rotN - else: - raise - elif op[1] == 'tr': - mCN = reCN.match(op[2]) # Fuck van Rossum for not having assignments inside expressions - if op[2] == 'σ_z': - for t in targets: - TMatrices[:,t] = qpms.apply_ndmatrix_left(zfl,qpms.apply_ndmatrix_left(zfl, TMatrices[:,t], (-4,-3)),(-2,-1)) - elif op[2] == 'σ_y': - for t in targets: - TMatrices[:,t] = qpms.apply_ndmatrix_left(yfl,qpms.apply_ndmatrix_left(yfl, TMatrices[:,t], (-4,-3)),(-2,-1)) - elif op[2] == 'σ_x': - for t in targets: - TMatrices[:,t] = qpms.apply_ndmatrix_left(xfl,qpms.apply_ndmatrix_left(xfl, TMatrices[:,t], (-4,-3)),(-2,-1)) - elif op[2] == 'C2': - for t in targets: - TMatrices[:,t] = qpms.apply_matrix_left(c2rot,qpms.apply_matrix_left(c2rot, TMatrices[:,t], -3),-1) - elif mCN: - rotN = int(mCN.group(2)) - power = int(mCN.group(1)) if mCN.group(1) else 1 - TMatrix_contribs = np.empty((rotN,TMatrices.shape[0],2,nelem,2,nelem), dtype=np.complex_) - for t in targets: - rotangle = 2*np.pi*power/rotN - rot = qpms.WignerD_yy_fromvector(lMax, np.array([0,0,rotangle])) - rotinv = qpms.WignerD_yy_fromvector(lMax, np.array([0,0,-rotangle])) - TMatrices[:,t] = qpms.apply_matrix_left(rot, qpms.apply_matrix_left(rotinv, TMatrices[:,t], -3),-1) - else: - raise - elif op[1] == 'copy': - raise # not implemented - elif op[1] == 'mult': - raise # not implemented - elif op[1] == 'multl': - incy = np.full((nelem,), False, dtype=bool) - for incl in op[2][0].split(','): - l = int(incl) - incy += (l == ny) - scaty = np.full((nelem,), False, dtype=bool) - for scatl in op[2][1].split(','): - l = int(scatl) - scaty += (l == ny) - for t in targets: - TMatrices[np.ix_(np.arange(TMatrices.shape[0]),np.array([t]),np.array([0,1]),scaty,np.array([0,1]),incy)] *= float(op[2][2]) - else: - raise #unknown operation; should not happen - -TMatrices_interp = interpolate.interp1d(freqs_orig*interpfreqfactor, TMatrices, axis=0, kind='linear',fill_value="extrapolate") - - - -# In[4]: -if(pargs.plot_TMatrix): - om = np.linspace(np.min(freqs_orig), np.max(freqs_orig),100) - TMatrix0ip = np.reshape(TMatrices_interp(om)[:,0], (len(om), 2*nelem*2*nelem)) - f, axa = plt.subplots(2, 2, figsize=(15,15)) - - #print(TMatrices.shape) - #plt.plot(om, TMatrices[:,0,0,0,0].imag,'r',om, TMatrices[:,0,0,0,0].real,'r--',om, TMatrices[:,0,2,0,2].imag,'b',om, TMatrices[:,0,2,0,2].real,'b--')) - - ax = axa[0,0] - ax2 = ax.twiny() - ax2.set_xlim([ax.get_xlim()[0]/eV*hbar,ax.get_xlim()[1]/eV*hbar]) - ax.plot( - om, TMatrix0ip[:,:].imag,'-',om, TMatrix0ip[:,:].real,'--', - ) - ax = axa[0,1] - ax2 = ax.twiny() - ax2.set_xlim([ax.get_xlim()[0]/eV*hbar,ax.get_xlim()[1]/eV*hbar]) - ax.plot( - om, abs(TMatrix0ip[:,:]),'-' - ) - ax.set_yscale('log') - - ax = axa[1,1] - ax2 = ax.twiny() - ax2.set_xlim([ax.get_xlim()[0]/eV*hbar,ax.get_xlim()[1]/eV*hbar]) - ax.plot( - om, np.unwrap(np.angle(TMatrix0ip[:,:]),axis=0),'-' - ) - - ax = axa[1,0] - ax.text(0.5,0.5,str(pargs).replace(',',',\n'),horizontalalignment='center',verticalalignment='center',transform=ax.transAxes) - pdf.savefig(f) - - -# In[ ]: - -''' -#kdensity = 66 #defined from cl arguments -bz_0 = np.array((0,0,0.,)) -bz_K1 = np.array((1.,0,0))*4*np.pi/3/hexside/s3 -bz_K2 = np.array((1./2.,s3/2,0))*4*np.pi/3/hexside/s3 -bz_M = np.array((3./4, s3/4,0))*4*np.pi/3/hexside/s3 -k0Mlist = bz_0 + (bz_M-bz_0) * np.linspace(0,1,kdensity)[:,nx] -kMK1list = bz_M + (bz_K1-bz_M) * np.linspace(0,1,kdensity)[:,nx] -kK10list = bz_K1 + (bz_0-bz_K1) * np.linspace(0,1,kdensity)[:,nx] -k0K2list = bz_0 + (bz_K2-bz_0) * np.linspace(0,1,kdensity)[:,nx] -kK2Mlist = bz_K2 + (bz_M-bz_K2) * np.linspace(0,1,kdensity)[:,nx] -B1 = 2* bz_K1 - bz_K2 -B2 = 2* bz_K2 - bz_K1 -klist = np.concatenate((k0Mlist,kMK1list,kK10list,k0K2list,kK2Mlist), axis=0) -kxmaplist = np.concatenate((np.array([0]),np.cumsum(np.linalg.norm(np.diff(klist, axis=0), axis=-1)))) -''' -klist = qpms.generate_trianglepoints(kdensity, v3d=True, include_origin=True)*3*math.pi/(3*kdensity*hexside) -TMatrices_om = TMatrices_interp(freq) - -svdres = qpms.hexlattice_zsym_getSVD(lMax=lMax, TMatrices_om=TMatrices_om, epsilon_b=epsilon_b, hexside=hexside, maxlayer=maxlayer, - omega=freq, klist=klist, gaussianSigma=gaussianSigma, onlyNmin=(0 if svdout else svn)) -if svdout: - ((svUfullTElist, svSfullTElist, svVfullTElist), (svUfullTMlist, svSfullTMlist, svVfullTMlist)) = svdres - (minsvElist, minsvTMlist) = (svSfullTElist[...,-svn:], svSfullTMlist[...,-svn:]) -else: - minsvTElist, minsvTMlist = svdres - - - -''' The new pretty diffracted order drawing ''' -maxlayer_reciprocal=4 -cdn = c/ math.sqrt(epsilon_b) -bz_0 = np.array((0,0,)) -bz_K1 = np.array((1.,0))*4*np.pi/3/hexside/s3 -bz_K2 = np.array((1./2.,s3/2))*4*np.pi/3/hexside/s3 -bz_M = np.array((3./4, s3/4))*4*np.pi/3/hexside/s3 - -# reciprocal lattice basis -B1 = 2* bz_K1 - bz_K2 -B2 = 2* bz_K2 - bz_K1 - -if svdout: - np.savez(svdout, omega = freq, klist = klist, bzpoints = np.array([bz_0, bz_K1, bz_K2, bz_M, B1, B2]), - uTE = svUfullTElist, - vTE = svVfullTElist, - sTE = svSfullTElist, - uTM = svUfullTMlist, - vTM = svVfullTMlist, - sTM = svSfullTMlist, - ) - -k2density = 100 -k0Mlist = bz_0 + (bz_M-bz_0) * np.linspace(0,1,k2density)[:,nx] -kMK1list = bz_M + (bz_K1-bz_M) * np.linspace(0,1,k2density)[:,nx] -kK10list = bz_K1 + (bz_0-bz_K1) * np.linspace(0,1,k2density)[:,nx] -k0K2list = bz_0 + (bz_K2-bz_0) * np.linspace(0,1,k2density)[:,nx] -kK2Mlist = bz_K2 + (bz_M-bz_K2) * np.linspace(0,1,k2density)[:,nx] -k2list = np.concatenate((k0Mlist,kMK1list,kK10list,k0K2list,kK2Mlist), axis=0) -kxmaplist = np.concatenate((np.array([0]),np.cumsum(np.linalg.norm(np.diff(k2list, axis=0), axis=-1)))) - -centers2=qpms.generate_trianglepoints(maxlayer_reciprocal, v3d = False, include_origin= True)*4*np.pi/3/hexside -rot90 = np.array([[0,-1],[1,0]]) -centers2=np.dot(centers2,rot90) - -import matplotlib.pyplot as plt -import matplotlib -from matplotlib.path import Path -import matplotlib.patches as patches -cmap = matplotlib.cm.prism -colormax = np.amax(np.linalg.norm(centers2,axis=0)) - - -# In[ ]: -for minN in reversed(range(svn)): - f, axes = plt.subplots(1,3, figsize=(20,4.8)) - ax = axes[0] - sc = ax.scatter(klist[:,0], klist[:,1], c = np.clip(np.abs(minsvTElist[:,minN]),0,1), lw=0) - for center in centers2: - circle=plt.Circle((center[0],center[1]),omega/cdn, facecolor='none', edgecolor=cmap(np.linalg.norm(center)/colormax),lw=0.5) - ax.add_artist(circle) - verts = [(math.cos(math.pi*i/3)*4*np.pi/3/hexside/s3,math.sin(math.pi*i/3)*4*np.pi/3/hexside/s3) for i in range(6 +1)] - codes = [Path.MOVETO,Path.LINETO,Path.LINETO,Path.LINETO,Path.LINETO,Path.LINETO,Path.CLOSEPOLY,] - path = Path(verts, codes) - patch = patches.PathPatch(path, facecolor='none', edgecolor='black', lw=1) - ax.add_patch(patch) - ax.set_xticks([]) - ax.set_yticks([]) - ax.title.set_text('E in-plane ("TE")') - f.colorbar(sc,ax=ax) - - - ax = axes[1] - sc = ax.scatter(klist[:,0], klist[:,1], c = np.clip(np.abs(minsvTMlist[:,minN]),0,1), lw=0) - for center in centers2: - circle=plt.Circle((center[0],center[1]),omega/cdn, facecolor='none', edgecolor=cmap(np.linalg.norm(center)/colormax),lw=0.5) - ax.add_artist(circle) - verts = [(math.cos(math.pi*i/3)*4*np.pi/3/hexside/s3,math.sin(math.pi*i/3)*4*np.pi/3/hexside/s3) for i in range(6 +1)] - codes = [Path.MOVETO,Path.LINETO,Path.LINETO,Path.LINETO,Path.LINETO,Path.LINETO,Path.CLOSEPOLY,] - path = Path(verts, codes) - patch = patches.PathPatch(path, facecolor='none', edgecolor='black', lw=1) - ax.add_patch(patch) - ax.set_xticks([]) - ax.set_yticks([]) - ax.title.set_text('E perpendicular ("TM")') - f.colorbar(sc,ax=ax) - - ax = axes[2] - for center in centers2: - ax.plot(kxmaplist, np.linalg.norm(k2list-center,axis=-1)*cdn, '-', color=cmap(np.linalg.norm(center)/colormax)) - - #ax.set_xlim([np.min(kxmlarr),np.max(kxmlarr)]) - #ax.set_ylim([np.min(omegalist),np.max(omegalist)]) - xticklist = [0, kxmaplist[len(k0Mlist)-1], kxmaplist[len(k0Mlist)+len(kMK1list)-1], kxmaplist[len(k0Mlist)+len(kMK1list)+len(kK10list)-1], kxmaplist[len(k0Mlist)+len(kMK1list)+len(kK10list)+len(k0K2list)-1], kxmaplist[len(k0Mlist)+len(kMK1list)+len(kK10list)+len(k0K2list)+len(kK2Mlist)-1]] - ax.set_xticks(xticklist) - for xt in xticklist: - ax.axvline(xt, ls='dotted', lw=0.3,c='k') - ax.set_xticklabels(['Γ', 'M', 'K', 'Γ', 'K\'','M']) - ax.axhline(omega, c='black') - ax.set_ylim([0,5e15]) - ax2 = ax.twinx() - ax2.set_ylim([ax.get_ylim()[0]/eV*hbar,ax.get_ylim()[1]/eV*hbar]) - - pdf.savefig(f) - -pdf.close() - -if scp_dest: - subprocess.run(['scp', pdfout, scp_dest]) - if svdout: - subprocess.run(['scp', svdout, scp_dest]) - -print(time.strftime("%H.%M:%S",time.gmtime(time.time()-begtime))) diff --git a/misc/dispersion_hex_chunks.py b/misc/dispersion_hex_chunks.py deleted file mode 100755 index 3168c35..0000000 --- a/misc/dispersion_hex_chunks.py +++ /dev/null @@ -1,239 +0,0 @@ -#!/usr/bin/env python3 - -import argparse, re, random, string -import subprocess -from scipy.constants import hbar, e as eV, pi, c - -def make_action_sharedlist(opname, listname): - class opAction(argparse.Action): - def __call__(self, parser, args, values, option_string=None): - if (not hasattr(args, listname)) or getattr(args, listname) is None: - setattr(args, listname, list()) - getattr(args,listname).append((opname, values)) - return opAction - -parser = argparse.ArgumentParser() -#TODO? použít type=argparse.FileType('r') ? -parser.add_argument('--TMatrix', action='store', required=True, help='Path to TMatrix file') -#parser.add_argument('--griddir', action='store', required=True, help='Path to the directory with precalculated translation operators') -parser.add_argument('--output_prefix', action='store', required=True, help='Prefix to the npz output (will be appended frequency, hexside and chunkno)') -#sizepar = parser.add_mutually_exclusive_group(required=True) -parser.add_argument('--hexside', action='store', type=float, required=True, help='Lattice hexagon size length') -parser.add_argument('--plot_TMatrix', action='store_true', help='Visualise TMatrix on the first page of the output') -#parser.add_argument('--SVD_output', action='store', help='Path to output singular value decomposition result') -parser.add_argument('--maxlayer', action='store', type=int, default=100, help='How far to sum the lattice points to obtain the dispersion') -parser.add_argument('--scp_to', action='store', metavar='N', type=str, help='SCP the output files to a given destination') -parser.add_argument('--background_permittivity', action='store', type=float, default=1., help='Background medium relative permittivity (default 1)') -parser.add_argument('--eVfreq', action='store', required=True, type=float, help='Frequency in eV') -parser.add_argument('--kdensity', action='store', type=int, default=33, help='Number of k-points per x-axis segment') -parser.add_argument('--chunklen', action='store', type=int, default=1000, help='Number of k-points per output file (default 1000)') -parser.add_argument('--lMax', action='store', type=int, help='Override lMax from the TMatrix file') -#TODO some more sophisticated x axis definitions -parser.add_argument('--gaussian', action='store', type=float, metavar='σ', help='Use a gaussian envelope for weighting the interaction matrix contributions (depending on the distance), measured in unit cell lengths (?) FIxME).') -parser.add_argument('--verbose', '-v', action='count', help='Be verbose (about computation times, mostly)') -popgrp=parser.add_argument_group(title='Operations') -popgrp.add_argument('--tr', dest='ops', action=make_action_sharedlist('tr', 'ops'), default=list()) # the default value for dest can be set once -popgrp.add_argument('--tr0', dest='ops', action=make_action_sharedlist('tr0', 'ops')) -popgrp.add_argument('--tr1', dest='ops', action=make_action_sharedlist('tr1', 'ops')) -popgrp.add_argument('--sym', dest='ops', action=make_action_sharedlist('sym', 'ops')) -popgrp.add_argument('--sym0', dest='ops', action=make_action_sharedlist('sym0', 'ops')) -popgrp.add_argument('--sym1', dest='ops', action=make_action_sharedlist('sym1', 'ops')) -#popgrp.add_argument('--mult', dest='ops', nargs=3, metavar=('INCSPEC', 'SCATSPEC', 'MULTIPLIER'), action=make_action_sharedlist('mult', 'ops')) -#popgrp.add_argument('--mult0', dest='ops', nargs=3, metavar=('INCSPEC', 'SCATSPEC', 'MULTIPLIER'), action=make_action_sharedlist('mult0', 'ops')) -#popgrp.add_argument('--mult1', dest='ops', nargs=3, metavar=('INCSPEC', 'SCATSPEC', 'MULTIPLIER'), action=make_action_sharedlist('mult1', 'ops')) -popgrp.add_argument('--multl', dest='ops', nargs=3, metavar=('INCL[,INCL,...]', 'SCATL[,SCATL,...]', 'MULTIPLIER'), action=make_action_sharedlist('multl', 'ops')) -popgrp.add_argument('--multl0', dest='ops', nargs=3, metavar=('INCL[,INCL,...]', 'SCATL[,SCATL,...]', 'MULTIPLIER'), action=make_action_sharedlist('multl0', 'ops')) -popgrp.add_argument('--multl1', dest='ops', nargs=3, metavar=('INCL[,INCL,...]', 'SCATL[,SCATL,...]', 'MULTIPLIER'), action=make_action_sharedlist('multl1', 'ops')) -parser.add_argument('--frequency_multiplier', action='store', type=float, default=1., help='Multiplies the frequencies in the TMatrix file by a given factor.') -# TODO enable more flexible per-sublattice specification -pargs=parser.parse_args() -print(pargs) - -maxlayer=pargs.maxlayer -hexside=pargs.hexside -eVfreq = pargs.eVfreq -freq = eVfreq*eV/hbar -verbose=pargs.verbose - -TMatrix_file = pargs.TMatrix - -epsilon_b = pargs.background_permittivity #2.3104 -gaussianSigma = pargs.gaussian if pargs.gaussian else None # hexside * 222 / 7 -interpfreqfactor = pargs.frequency_multiplier -scp_dest = pargs.scp_to if pargs.scp_to else None -kdensity = pargs.kdensity -chunklen = pargs.chunklen - -ops = list() -opre = re.compile('(tr|sym|copy|multl|mult)(\d*)') -for oparg in pargs.ops: - opm = opre.match(oparg[0]) - if opm: - ops.append(((opm.group(2),) if opm.group(2) else (0,1), opm.group(1), oparg[1])) - else: - raise # should not happen -print(ops) - - -# -----------------finished basic CLI parsing (except for op arguments) ------------------ -from qpms.timetrack import _time_b, _time_e -btime=_time_b(verbose) - -import qpms -import numpy as np -import os, sys, warnings, math -from scipy import interpolate -nx = None -s3 = math.sqrt(3) - - -# specifikace T-matice zde -cdn = c/ math.sqrt(epsilon_b) -TMatrices_orig, freqs_orig, freqs_weirdunits_orig, lMaxTM = qpms.loadScuffTMatrices(TMatrix_file) -lMax = lMaxTM -if pargs.lMax: - lMax = pargs.lMax if pargs.lMax else lMaxTM -my, ny = qpms.get_mn_y(lMax) -nelem = len(my) -if pargs.lMax: #force commandline specified lMax - TMatrices_orig = TMatrices_orig[...,0:nelem,:,0:nelem] - -TMatrices = np.array(np.broadcast_to(TMatrices_orig[:,nx,:,:,:,:],(len(freqs_orig),2,2,nelem,2,nelem)) ) - -#TMatrices[:,:,:,:,:,ny==3] *= factor13inc -#TMatrices[:,:,:,ny==3,:,:] *= factor13scat -xfl = qpms.xflip_tyty(lMax) -yfl = qpms.yflip_tyty(lMax) -zfl = qpms.zflip_tyty(lMax) -c2rot = qpms.apply_matrix_left(qpms.yflip_yy(3),qpms.xflip_yy(3),-1) - -reCN = re.compile('(\d*)C(\d+)') -#TODO C nekonečno - -for op in ops: - if op[0] == 'all': - targets = (0,1) - elif isinstance(op[0],int): - targets = (op[0],) - else: - targets = op[0] - - if op[1] == 'sym': - mCN = reCN.match(op[2]) # Fuck van Rossum for not having assignments inside expressions - if op[2] == 'σ_z': - for t in targets: - TMatrices[:,t] = (TMatrices[:,t] + qpms.apply_ndmatrix_left(zfl,qpms.apply_ndmatrix_left(zfl, TMatrices[:,t], (-4,-3)),(-2,-1)))/2 - elif op[2] == 'σ_y': - for t in targets: - TMatrices[:,t] = (TMatrices[:,t] + qpms.apply_ndmatrix_left(yfl,qpms.apply_ndmatrix_left(yfl, TMatrices[:,t], (-4,-3)),(-2,-1)))/2 - elif op[2] == 'σ_x': - for t in targets: - TMatrices[:,t] = (TMatrices[:,t] + qpms.apply_ndmatrix_left(xfl,qpms.apply_ndmatrix_left(xfl, TMatrices[:,t], (-4,-3)),(-2,-1)))/2 - elif op[2] == 'C2': # special case of the latter - for t in targets: - TMatrices[:,t] = (TMatrices[:,t] + qpms.apply_matrix_left(c2rot,qpms.apply_matrix_left(c2rot, TMatrices[:,t], -3),-1))/2 - elif mCN: - rotN = int(mCN.group(2)) - TMatrix_contribs = np.empty((rotN,TMatrices.shape[0],2,nelem,2,nelem), dtype=np.complex_) - for t in targets: - for i in range(rotN): - rotangle = 2*np.pi*i / rotN - rot = qpms.WignerD_yy_fromvector(lMax,np.array([0,0,rotangle])) - rotinv = qpms.WignerD_yy_fromvector(lMax,np.array([0,0,-rotangle])) - TMatrix_contribs[i] = qpms.apply_matrix_left(rot,qpms.apply_matrix_left(rotinv, TMatrices[:,t], -3),-1) - TMatrices[:,t] = np.sum(TMatrix_contribs, axis=0) / rotN - else: - raise - elif op[1] == 'tr': - mCN = reCN.match(op[2]) # Fuck van Rossum for not having assignments inside expressions - if op[2] == 'σ_z': - for t in targets: - TMatrices[:,t] = qpms.apply_ndmatrix_left(zfl,qpms.apply_ndmatrix_left(zfl, TMatrices[:,t], (-4,-3)),(-2,-1)) - elif op[2] == 'σ_y': - for t in targets: - TMatrices[:,t] = qpms.apply_ndmatrix_left(yfl,qpms.apply_ndmatrix_left(yfl, TMatrices[:,t], (-4,-3)),(-2,-1)) - elif op[2] == 'σ_x': - for t in targets: - TMatrices[:,t] = qpms.apply_ndmatrix_left(xfl,qpms.apply_ndmatrix_left(xfl, TMatrices[:,t], (-4,-3)),(-2,-1)) - elif op[2] == 'C2': - for t in targets: - TMatrices[:,t] = qpms.apply_matrix_left(c2rot,qpms.apply_matrix_left(c2rot, TMatrices[:,t], -3),-1) - elif mCN: - rotN = int(mCN.group(2)) - power = int(mCN.group(1)) if mCN.group(1) else 1 - TMatrix_contribs = np.empty((rotN,TMatrices.shape[0],2,nelem,2,nelem), dtype=np.complex_) - for t in targets: - rotangle = 2*np.pi*power/rotN - rot = qpms.WignerD_yy_fromvector(lMax, np.array([0,0,rotangle])) - rotinv = qpms.WignerD_yy_fromvector(lMax, np.array([0,0,-rotangle])) - TMatrices[:,t] = qpms.apply_matrix_left(rot, qpms.apply_matrix_left(rotinv, TMatrices[:,t], -3),-1) - else: - raise - elif op[1] == 'copy': - raise # not implemented - elif op[1] == 'mult': - raise # not implemented - elif op[1] == 'multl': - incy = np.full((nelem,), False, dtype=bool) - for incl in op[2][0].split(','): - l = int(incl) - incy += (l == ny) - scaty = np.full((nelem,), False, dtype=bool) - for scatl in op[2][1].split(','): - l = int(scatl) - scaty += (l == ny) - for t in targets: - TMatrices[np.ix_(np.arange(TMatrices.shape[0]),np.array([t]),np.array([0,1]),scaty,np.array([0,1]),incy)] *= float(op[2][2]) - else: - raise #unknown operation; should not happen - -TMatrices_interp = interpolate.interp1d(freqs_orig*interpfreqfactor, TMatrices, axis=0, kind='linear',fill_value="extrapolate") - -klist_full = qpms.generate_trianglepoints(kdensity, v3d=True, include_origin=True)*3*math.pi/(3*kdensity*hexside) -TMatrices_om = TMatrices_interp(freq) - -chunkn = math.ceil(klist_full.shape[0] / chunklen) - -if verbose: - print('Evaluating %d k-points in %d chunks' % (klist_full.shape[0], chunkn), file = sys.stderr) - sys.stderr.flush() - -metadata = np.array({ - 'lMax' : lMax, - 'maxlayer' : maxlayer, - 'gaussianSigma' : gaussianSigma, - 'epsilon_b' : epsilon_b, - 'hexside' : hexside, - 'chunkn' : chunkn, - 'TMatrix_file' : TMatrix_file, - 'ops' : ops, - }) - -for chunki in range(chunkn): - svdout = '%s_%dnm_%.4f_c%03d.npz' % (pargs.output_prefix, hexside/1e-9, eVfreq, chunki) - - klist = klist_full[chunki * chunklen : (chunki + 1) * chunklen] - - svdres = qpms.hexlattice_zsym_getSVD(lMax=lMax, TMatrices_om=TMatrices_om, epsilon_b=epsilon_b, hexside=hexside, maxlayer=maxlayer, - omega=freq, klist=klist, gaussianSigma=gaussianSigma, onlyNmin=False, verbose=verbose) - - #((svUfullTElist, svSfullTElist, svVfullTElist), (svUfullTMlist, svSfullTMlist, svVfullTMlist)) = svdres - - np.savez(svdout, omega = freq, klist = klist, - metadata=metadata, - uTE = svdres[0][0], - vTE = svdres[0][2], - sTE = svdres[0][1], - uTM = svdres[1][0], - vTM = svdres[1][2], - sTM = svdres[1][1], - - ) - svdres=None - - if scp_dest: - if svdout: - subprocess.run(['scp', svdout, scp_dest]) - -_time_e(btime, verbose) -#print(time.strftime("%H.%M:%S",time.gmtime(time.time()-begtime))) diff --git a/misc/finitesqlatzsym-scatter.py b/misc/finitesqlatzsym-scatter.py deleted file mode 100755 index ccc5898..0000000 --- a/misc/finitesqlatzsym-scatter.py +++ /dev/null @@ -1,376 +0,0 @@ -#!/usr/bin/env python3 - -import argparse, re, random, string, sys -import subprocess -import warnings -from scipy.constants import hbar, e as eV, pi, c - -unitcell_size = 1 # rectangular lattice -unitcell_indices = tuple(range(unitcell_size)) - -def make_action_sharedlist(opname, listname): - class opAction(argparse.Action): - def __call__(self, parser, args, values, option_string=None): - if (not hasattr(args, listname)) or getattr(args, listname) is None: - setattr(args, listname, list()) - getattr(args,listname).append((opname, values)) - return opAction - -parser = argparse.ArgumentParser() -#TODO? použít type=argparse.FileType('r') ? -parser.add_argument('--TMatrix', action='store', required=True, help='Path to TMatrix file') -#parser.add_argument('--griddir', action='store', required=True, help='Path to the directory with precalculated translation operators') -parser.add_argument('--output_prefix', '-p', '-o', action='store', required=True, help='Prefix to the npz output (will be appended frequency, hexside and chunkno)') -parser.add_argument('--nosuffix', action='store_true', help='Do not add dimension metadata to the output filenames') -#sizepar = parser.add_mutually_exclusive_group(required=True) -#parser.add_argument('--hexside', action='store', type=float, required=True, help='Lattice hexagon size length') -parser.add_argument('--dx', action='store', type=float, required=True, help='x-direction lattice constant') -parser.add_argument('--dy', action='store', type=float, required=True, help='y-direction lattice constant') - -parser.add_argument('--Nx', '--nx', action='store', type=int, required=True, help='Lattice points in the x-direction') -parser.add_argument('--Ny', '--ny', action='store', type=int, required=True, help='Lattice points in the y-direction') - -# In these default settings, the area is 2x2 times larger than first BZ -parser.add_argument('--kxmin', action='store', type=float, default=-1., help='TODO') -parser.add_argument('--kxmax', action='store', type=float, default=1., help='TODO') -parser.add_argument('--kymin', action='store', type=float, default=-1., help='TODO') -parser.add_argument('--kymax', action='store', type=float, default=1., help='TODO') - -#parser.add_argument('--kdensity', action='store', type=int, default=33, help='Number of k-points per x-axis segment') -parser.add_argument('--kxdensity', action='store', type=int, default=51, help='k-space resolution in the x-direction') -parser.add_argument('--kydensity', action='store', type=int, default=51, help='k-space resolution in the y-direction') - -partgrp = parser.add_mutually_exclusive_group() -partgrp.add_argument('--only_TE', action='store_true', help='Calculate only the projection on the E⟂z modes') -partgrp.add_argument('--only_TM', action='store_true', help='Calculate only the projection on the E∥z modes') -partgrp.add_argument('--serial', action='store_true', help='Calculate the TE and TM parts separately to save memory') - -parser.add_argument('--nocentre', action='store_true', help='Place the coordinate origin to the left bottom corner rather that to the centre of the array') - -parser.add_argument('--plot_TMatrix', action='store_true', help='Visualise TMatrix on the first page of the output') -#parser.add_argument('--SVD_output', action='store', help='Path to output singular value decomposition result') -parser.add_argument('--maxlayer', action='store', type=int, default=100, help='How far to sum the lattice points to obtain the dispersion') -parser.add_argument('--scp_to', action='store', metavar='N', type=str, help='SCP the output files to a given destination') -parser.add_argument('--background_permittivity', action='store', type=float, default=1., help='Background medium relative permittivity (default 1)') -parser.add_argument('--eVfreq', action='store', required=True, type=float, help='Frequency in eV') - -parser.add_argument('--chunklen', action='store', type=int, default=3000, help='Number of k-points per output file (default 3000)') -parser.add_argument('--lMax', action='store', type=int, help='Override lMax from the TMatrix file') -#TODO some more sophisticated x axis definitions -#parser.add_argument('--gaussian', action='store', type=float, metavar='σ', help='Use a gaussian envelope for weighting the interaction matrix contributions (depending on the distance), measured in unit cell lengths (?) FIxME).') -parser.add_argument('--verbose', '-v', action='count', help='Be verbose (about computation times, mostly)') -popgrp=parser.add_argument_group(title='Operations') -popgrp.add_argument('--tr', dest='ops', action=make_action_sharedlist('tr', 'ops'), default=list()) # the default value for dest can be set once -for i in unitcell_indices: - popgrp.add_argument('--tr%d'%i, dest='ops', action=make_action_sharedlist('tr%d'%i, 'ops')) -popgrp.add_argument('--sym', dest='ops', action=make_action_sharedlist('sym', 'ops')) -for i in unitcell_indices: - popgrp.add_argument('--sym%d'%i, dest='ops', action=make_action_sharedlist('sym%d'%i, 'ops')) -#popgrp.add_argument('--mult', dest='ops', nargs=3, metavar=('INCSPEC', 'SCATSPEC', 'MULTIPLIER'), action=make_action_sharedlist('mult', 'ops')) -#popgrp.add_argument('--mult0', dest='ops', nargs=3, metavar=('INCSPEC', 'SCATSPEC', 'MULTIPLIER'), action=make_action_sharedlist('mult0', 'ops')) -#popgrp.add_argument('--mult1', dest='ops', nargs=3, metavar=('INCSPEC', 'SCATSPEC', 'MULTIPLIER'), action=make_action_sharedlist('mult1', 'ops')) -popgrp.add_argument('--multl', dest='ops', nargs=3, metavar=('INCL[,INCL,...]', 'SCATL[,SCATL,...]', 'MULTIPLIER'), action=make_action_sharedlist('multl', 'ops')) -for i in unitcell_indices: - popgrp.add_argument('--multl%d'%i, dest='ops', nargs=3, metavar=('INCL[,INCL,...]', 'SCATL[,SCATL,...]', 'MULTIPLIER'), action=make_action_sharedlist('multl%d'%i, 'ops')) -#popgrp.add_argument('--multl1', dest='ops', nargs=3, metavar=('INCL[,INCL,...]', 'SCATL[,SCATL,...]', 'MULTIPLIER'), action=make_action_sharedlist('multl1', 'ops')) -parser.add_argument('--frequency_multiplier', action='store', type=float, default=1., help='Multiplies the frequencies in the TMatrix file by a given factor.') -# TODO enable more flexible per-sublattice specification -pargs=parser.parse_args() -if pargs.verbose: - print(pargs, file = sys.stderr) - -maxlayer=pargs.maxlayer -eVfreq = pargs.eVfreq -freq = eVfreq*eV/hbar -verbose=pargs.verbose -dy = pargs.dy -dx = pargs.dx -Ny = pargs.Ny -Nx = pargs.Nx - -TMatrix_file = pargs.TMatrix - -epsilon_b = pargs.background_permittivity #2.3104 -#gaussianSigma = pargs.gaussian if pargs.gaussian else None # hexside * 222 / 7 -interpfreqfactor = pargs.frequency_multiplier -scp_dest = pargs.scp_to if pargs.scp_to else None -kxdensity = pargs.kxdensity -kydensity = pargs.kydensity -chunklen = pargs.chunklen - -ops = list() -opre = re.compile('(tr|sym|copy|multl|mult)(\d*)') -for oparg in pargs.ops: - opm = opre.match(oparg[0]) - if opm: - ops.append(((opm.group(2),) if opm.group(2) else unitcell_indices, opm.group(1), oparg[1])) - else: - raise # should not happen -if(verbose): - print(ops, file = sys.stderr) - - -# -----------------finished basic CLI parsing (except for op arguments) ------------------ -from qpms.timetrack import _time_b, _time_e -btime=_time_b(verbose) - -import qpms -import numpy as np -import os, warnings, math -from scipy import interpolate -nx = None -s3 = math.sqrt(3) - - -# specifikace T-matice zde -refind = math.sqrt(epsilon_b) -cdn = c / refind -k_0 = freq * refind / c # = freq / cdn -TMatrices_orig, freqs_orig, freqs_weirdunits_orig, lMaxTM = qpms.loadScuffTMatrices(TMatrix_file) -lMax = lMaxTM -if pargs.lMax: - lMax = pargs.lMax if pargs.lMax else lMaxTM -my, ny = qpms.get_mn_y(lMax) -nelem = len(my) -if pargs.lMax: #force commandline specified lMax - TMatrices_orig = TMatrices_orig[...,0:nelem,:,0:nelem] -TMatrices = np.array(np.broadcast_to(TMatrices_orig[:,nx,:,:,:,:],(len(freqs_orig),unitcell_size,2,nelem,2,nelem)) ) -xfl = qpms.xflip_tyty(lMax) -yfl = qpms.yflip_tyty(lMax) -zfl = qpms.zflip_tyty(lMax) -c2rot = qpms.apply_matrix_left(qpms.yflip_yy(3),qpms.xflip_yy(3),-1) - -reCN = re.compile('(\d*)C(\d+)') -#TODO C nekonečno - -for op in ops: - if op[0] == 'all': - #targets = (0,1) - targets = unitcell_indices - elif isinstance(op[0],int): - targets = (op[0],) - else: - targets = op[0] - - if op[1] == 'sym': - mCN = reCN.match(op[2]) # Fuck van Rossum for not having assignments inside expressions - if op[2] == 'σ_z': - for t in targets: - TMatrices[:,t] = (TMatrices[:,t] + qpms.apply_ndmatrix_left(zfl,qpms.apply_ndmatrix_left(zfl, TMatrices[:,t], (-4,-3)),(-2,-1)))/2 - elif op[2] == 'σ_y': - for t in targets: - TMatrices[:,t] = (TMatrices[:,t] + qpms.apply_ndmatrix_left(yfl,qpms.apply_ndmatrix_left(yfl, TMatrices[:,t], (-4,-3)),(-2,-1)))/2 - elif op[2] == 'σ_x': - for t in targets: - TMatrices[:,t] = (TMatrices[:,t] + qpms.apply_ndmatrix_left(xfl,qpms.apply_ndmatrix_left(xfl, TMatrices[:,t], (-4,-3)),(-2,-1)))/2 - elif op[2] == 'C2': # special case of the latter - for t in targets: - TMatrices[:,t] = (TMatrices[:,t] + qpms.apply_matrix_left(c2rot,qpms.apply_matrix_left(c2rot, TMatrices[:,t], -3),-1))/2 - elif mCN: - rotN = int(mCN.group(2)) - TMatrix_contribs = np.empty((rotN,TMatrices.shape[0],2,nelem,2,nelem), dtype=np.complex_) - for t in targets: - for i in range(rotN): - rotangle = 2*np.pi*i / rotN - rot = qpms.WignerD_yy_fromvector(lMax,np.array([0,0,rotangle])) - rotinv = qpms.WignerD_yy_fromvector(lMax,np.array([0,0,-rotangle])) - TMatrix_contribs[i] = qpms.apply_matrix_left(rot,qpms.apply_matrix_left(rotinv, TMatrices[:,t], -3),-1) - TMatrices[:,t] = np.sum(TMatrix_contribs, axis=0) / rotN - else: - raise - elif op[1] == 'tr': - mCN = reCN.match(op[2]) # Fuck van Rossum for not having assignments inside expressions - if op[2] == 'σ_z': - for t in targets: - TMatrices[:,t] = qpms.apply_ndmatrix_left(zfl,qpms.apply_ndmatrix_left(zfl, TMatrices[:,t], (-4,-3)),(-2,-1)) - elif op[2] == 'σ_y': - for t in targets: - TMatrices[:,t] = qpms.apply_ndmatrix_left(yfl,qpms.apply_ndmatrix_left(yfl, TMatrices[:,t], (-4,-3)),(-2,-1)) - elif op[2] == 'σ_x': - for t in targets: - TMatrices[:,t] = qpms.apply_ndmatrix_left(xfl,qpms.apply_ndmatrix_left(xfl, TMatrices[:,t], (-4,-3)),(-2,-1)) - elif op[2] == 'C2': - for t in targets: - TMatrices[:,t] = qpms.apply_matrix_left(c2rot,qpms.apply_matrix_left(c2rot, TMatrices[:,t], -3),-1) - elif mCN: - rotN = int(mCN.group(2)) - power = int(mCN.group(1)) if mCN.group(1) else 1 - TMatrix_contribs = np.empty((rotN,TMatrices.shape[0],2,nelem,2,nelem), dtype=np.complex_) - for t in targets: - rotangle = 2*np.pi*power/rotN - rot = qpms.WignerD_yy_fromvector(lMax, np.array([0,0,rotangle])) - rotinv = qpms.WignerD_yy_fromvector(lMax, np.array([0,0,-rotangle])) - TMatrices[:,t] = qpms.apply_matrix_left(rot, qpms.apply_matrix_left(rotinv, TMatrices[:,t], -3),-1) - else: - raise - elif op[1] == 'copy': - raise # not implemented - elif op[1] == 'mult': - raise # not implemented - elif op[1] == 'multl': - incy = np.full((nelem,), False, dtype=bool) - for incl in op[2][0].split(','): - l = int(incl) - incy += (l == ny) - scaty = np.full((nelem,), False, dtype=bool) - for scatl in op[2][1].split(','): - l = int(scatl) - scaty += (l == ny) - for t in targets: - TMatrices[np.ix_(np.arange(TMatrices.shape[0]),np.array([t]),np.array([0,1]),scaty,np.array([0,1]),incy)] *= float(op[2][2]) - else: - raise #unknown operation; should not happen - -TMatrices_interp = interpolate.interp1d(freqs_orig*interpfreqfactor, TMatrices, axis=0, kind='linear',fill_value="extrapolate") - - -xpositions = np.arange(Nx) * dx -ypositions = np.arange(Ny) * dy -if not pargs.nocentre: - xpositions -= Nx * dx / 2 - ypositions -= Ny * dy / 2 -xpositions, ypositions = np.meshgrid(xpositions, ypositions, indexing='ij', copy=False) -positions=np.stack((xpositions.ravel(),ypositions.ravel()), axis=-1) -positions=positions[np.random.permutation(len(positions))] -N = positions.shape[0] - -kx = np.linspace(pargs.kxmin, pargs.kxmax, num=pargs.kxdensity, endpoint=True) * 2*np.pi / dx -ky = np.linspace(pargs.kymin, pargs.kymax, num=pargs.kydensity, endpoint=True) * 2*np.pi / dy -kx, ky = np.meshgrid(kx, ky, indexing='ij', copy=False) -kz = np.sqrt(k_0**2 - (kx ** 2 + ky ** 2)) - -klist_full = np.stack((kx,ky,kz), axis=-1).reshape((-1,3)) -TMatrices_om = TMatrices_interp(freq) - -chunkn = math.ceil(klist_full.size / 3 / chunklen) - -if verbose: - print('Evaluating %d k-points' % klist_full.size + ('in %d chunks'%chunkn) if chunkn>1 else '' , file = sys.stderr) - sys.stderr.flush() - -try: - version = qpms.__version__ -except NameError: - version = None - -metadata = np.array({ - 'script': os.path.basename(__file__), - 'version': version, - 'type' : 'Plane wave scattering on a finite rectangular lattice', - 'lMax' : lMax, - 'dx' : dx, - 'dy' : dy, - 'Nx' : Nx, - 'Ny' : Ny, - #'maxlayer' : maxlayer, - #'gaussianSigma' : gaussianSigma, - 'epsilon_b' : epsilon_b, - #'hexside' : hexside, - 'chunkn' : chunkn, - 'chunki' : 0, - 'TMatrix_file' : TMatrix_file, - 'ops' : ops, - 'centred' : not pargs.nocentre - }) - - -scat = qpms.Scattering_2D_zsym(positions, TMatrices_om, k_0, verbose=verbose) - -if pargs.only_TE: - actions = (0,) -elif pargs.only_TM: - actions = (1,) -elif pargs.serial: - actions = (0,1) -else: - actions = (None,) - -xu = np.array((1,0,0)) -yu = np.array((0,1,0)) -zu = np.array((0,0,1)) -TEč, TMč = qpms.symz_indexarrays(lMax) - -klist_full_2D = klist_full[...,:2] -klist_full_dir = klist_full/np.linalg.norm(klist_full, axis=-1, keepdims=True) -for action in actions: - if action is None: - scat.prepare(verbose=verbose) - actionstring = '' - else: - scat.prepare_partial(action, verbose=verbose) - actionstring = '.TM' if action else '.TE' - for chunki in range(chunkn): - sbtime = _time_b(verbose, step='Solving the scattering problem, chunk %d'%chunki+actionstring) - if pargs.nosuffix: - outfile = pargs.output_prefix + actionstring + ( - ('.%03d' % chunki) if chunkn > 1 else '') - else: - outfile = '%s_%dx%d_%.0fnmx%.0fnm_%.4f%s%s.npz' % ( - pargs.output_prefix, Nx, Ny, dx/1e-9, dy/1e-9, - eVfreq, actionstring, - (".%03d" % chunki) if chunkn > 1 else '') - - klist = klist_full[chunki * chunklen : (chunki + 1) * chunklen] - klist2d = klist_full_2D[chunki * chunklen : (chunki + 1) * chunklen] - klistdir = klist_full_dir[chunki * chunklen : (chunki + 1) * chunklen] - - ''' - The following loop is a fuckup that has its roots in the fact that - the function qpms.get_π̃τ̃_y1 in qpms_p.py is not vectorized - (and consequently, neither is plane_pq_y.) - - And Scattering_2D_zsym.scatter_partial is not vectorized, either. - ''' - if action == 0 or action is None: - xresult = np.full((klist.shape[0], N, nelem), np.nan, dtype=complex) - yresult = np.full((klist.shape[0], N, nelem), np.nan, dtype=complex) - if action == 1 or action is None: - zresult = np.full((klist.shape[0], N, nelem), np.nan, dtype=complex) - for i in range(klist.shape[0]): - if math.isnan(klist[i,2]): - if(verbose): - print("%d. momentum %s invalid (k_0=%f), skipping" % (i, str(klist[i]),k_0)) - continue - kdir = klistdir[i] - phases = np.exp(-1j*np.sum(klist2d[i] * positions, axis=-1)) - if action == 0 or action is None: - pq = np.array(qpms.plane_pq_y(lMax, kdir, xu)).ravel()[TEč] * phases[:, nx] - xresult[i] = scat.scatter_partial(0, pq) - pq = np.array(qpms.plane_pq_y(lMax, kdir, yu)).ravel()[TEč] * phases[:, nx] - yresult[i] = scat.scatter_partial(0, pq) - if action == 1 or action is None: - pq = np.array(qpms.plane_pq_y(lMax, kdir, zu)).ravel()[TMč] * phases[:, nx] - zresult[i] = scat.scatter_partial(1, pq) - _time_e(sbtime, verbose, step='Solving the scattering problem, chunk %d'%chunki+actionstring) - - metadata[()]['chunki'] = chunki - if action is None: - np.savez(outfile, omega = freq, klist = klist, - metadata=metadata, - positions=positions, - ab_x=xresult, - ab_y=yresult, - ab_z=zresult - ) - elif action == 0: - np.savez(outfile, omega = freq, klist = klist, - metadata=metadata, - positions=positions, - ab_x=xresult, - ab_y=yresult, - ) - elif action == 1: - np.savez(outfile, omega = freq, klist = klist, - metadata=metadata, - positions=positions, - ab_z=zresult - ) - else: - raise - - if scp_dest: - if outfile: - subprocess.run(['scp', outfile, scp_dest]) - scat.forget_matrices() # free memory in case --serial was used - -_time_e(btime, verbose) diff --git a/misc/generaldisp.py b/misc/generaldisp.py deleted file mode 100755 index 52bd5d7..0000000 --- a/misc/generaldisp.py +++ /dev/null @@ -1,340 +0,0 @@ -#!/usr/bin/env python3 -''' -Bulk SVD mode computation for compact scatterer 2D lattices -''' - -__TODOs__ = ''' -BIG TODO: Use more efficient way to calculate the interaction sums: perhaps some customized Ewald-type summation? - -Small TODOs: - - Implement a more user-friendly way to define the lattice base vectors and positions of the particles. - cf. https://stackoverflow.com/questions/2371436/evaluating-a-mathematical-expression-in-a-string/2371789 - - low priority: allow to perform some more custom operations on T-Matrix, using some kind of parsing from the previous point - - Autodetect symmetries - -''' -import argparse, re, random, string -import subprocess -from scipy.constants import hbar, e as eV, pi, c -import warnings - -def make_action_sharedlist(opname, listname): - class opAction(argparse.Action): - def __call__(self, parser, args, values, option_string=None): - if (not hasattr(args, listname)) or getattr(args, listname) is None: - setattr(args, listname, list()) - getattr(args,listname).append((opname, values)) - return opAction - -parser = argparse.ArgumentParser() -#TODO? použít type=argparse.FileType('r') ? -#TODO create some user-friendlier way to define lattice vectors, cf. https://stackoverflow.com/questions/2371436/evaluating-a-mathematical-expression-in-a-string/2371789 -parser.add_argument('--lattice_base', nargs=4, action='store', type=float, required=True, help='Lattice basis vectors x1, y1, x2, y2') -parser.add_argument('--particle', '-p', nargs='+', action=make_action_sharedlist('particle', 'particlespec'), help='Particle label, coordinates x,y, and (optionally) path to the T-Matrix.') -parser.add_argument('--TMatrix', '-t', nargs='+', action=make_action_sharedlist('TMatrix_path', 'particlespec'), help='Path to TMatrix file') -#parser.add_argument('--griddir', action='store', required=True, help='Path to the directory with precalculated translation operators') -parser.add_argument('--output_prefix', action='store', required=True, help='Prefix to the npz output (will be appended frequency, hexside and chunkno)') -#sizepar = parser.add_mutually_exclusive_group(required=True) -#DEL parser.add_argument('--hexside', action='store', type=float, required=True, help='Lattice hexagon size length') -parser.add_argument('--plot_TMatrix', action='store_true', help='Visualise TMatrix on the first page of the output') -#parser.add_argument('--SVD_output', action='store', help='Path to output singular value decomposition result') -parser.add_argument('--maxlayer', action='store', type=int, default=100, help='How far to sum the lattice points to obtain the dispersion') -parser.add_argument('--scp_to', action='store', metavar='N', type=str, help='SCP the output files to a given destination') -parser.add_argument('--background_permittivity', action='store', type=float, default=1., help='Background medium relative permittivity (default 1)') -parser.add_argument('--eVfreq', action='store', required=True, type=float, help='Frequency in eV') -parser.add_argument('--kdensity', '--k_density', action='store', type=int, default=33, help='Number of k-points per x-axis segment FIXME DESCRIPTION') -parser.add_argument('--bz_coverage', action='store', type=float, default=1., help='Brillouin zone coverage in relative length (default 1 for whole 1. BZ)') -parser.add_argument('--bz_edge_width', action='store', type=float, default=0., help='Width of the more densely covered belt along the 1. BZ edge in relative lengths') -parser.add_argument('--bz_edge_factor', action='store', type=float, default=8., help='Relative density of the belt along the 1. BZ edge w.r.t. k_density (default==8)') -parser.add_argument('--bz_edge_twoside', action='store_true', help='Compute also the parts of the densely covered edge belt outside the 1. BZ') -parser.add_argument('--bz_corner_width', action='store', type=float, default=0., help='Size of the more densely covered subcell along the 1. BZ corners in relative lengths') -parser.add_argument('--bz_corner_factor', action='store', type=float, default=16., help='Relative density of the subcell along the 1. BZ corner w.r.t. k_density (default==16)') -parser.add_argument('--bz_corner_twoside', action='store_true', help='Compute also the parts of the densely covered subcell outside the 1. BZ') - -parser.add_argument('--chunklen', action='store', type=int, default=1000, help='Number of k-points per output file (default 1000)') -parser.add_argument('--lMax', action=make_action_sharedlist('lMax', 'particlespec'), nargs=+, help='Override lMax from the TMatrix file') -#TODO some more sophisticated x axis definitions -parser.add_argument('--gaussian', action='store', type=float, metavar='σ', help='Use a gaussian envelope for weighting the interaction matrix contributions (depending on the distance), measured in unit cell lengths (?) FIxME).') -parser.add_argument('--verbose', '-v', action='count', help='Be verbose (about computation times, mostly)') -popgrp=parser.add_argument_group(title='Operations') -popgrp.add_argument('--tr', dest='ops', nargs='+', action=make_action_sharedlist('tr', 'ops'), default=list()) # the default value for dest can be set once -popgrp.add_argument('--sym', dest='ops', nargs='+', action=make_action_sharedlist('sym', 'ops')) -#popgrp.add_argument('--mult', dest='ops', nargs=3, metavar=('INCSPEC', 'SCATSPEC', 'MULTIPLIER'), action=make_action_sharedlist('mult', 'ops')) -#popgrp.add_argument('--multl', dest='ops', nargs=3, metavar=('INCL[,INCL,...]', 'SCATL[,SCATL,...]', 'MULTIPLIER'), action=make_action_sharedlist('multl', 'ops')) -parser.add_argument('--frequency_multiplier', action='store', type=float, default=1., help='Multiplies the frequencies in the TMatrix file by a given factor.') -pargs=parser.parse_args() -print(pargs) - -exit(0) ### - -maxlayer=pargs.maxlayer -#DEL hexside=pargs.hexside -eVfreq = pargs.eVfreq -freq = eVfreq*eV/hbar -verbose=pargs.verbose - -#DEL TMatrix_file = pargs.TMatrix - -epsilon_b = pargs.background_permittivity #2.3104 -gaussianSigma = pargs.gaussian if pargs.gaussian else None # hexside * 222 / 7 -interpfreqfactor = pargs.frequency_multiplier -scp_dest = pargs.scp_to if pargs.scp_to else None -kdensity = pargs.kdensity -chunklen = pargs.chunklen - -#### Nanoparticle position and T-matrix path parsing #### -TMatrix_paths = dict() -lMax_overrides = dict() -default_TMatrix_path = None -default_lMax_override = None -if not any((arg_type == 'particle') in (arg_type, arg_content) for in pargs.particlespec): - # no particles positions given: suppose only one per unit cell, in the cell origin - positions = {None: (0.0)} -else: - positions = dict() -for arg_type, arg_content in pargs.particlespec: - if arg_type == 'particle' # --particle option - if 3 <= len(arg_content) <= 4: - try: - positions[arg_content[0]] = (float(arg_content[1]), float(arg_content[2])) - except ValueError as e: - e.args += ("second and third argument of --particle must be valid floats, given: ", arg_content) - raise - if len(arg_content == 4): - if arg_content[0] in TMatrix_paths: - warnings.warn('T-matrix path for particle \'%s\' already specified.' - 'Overriding with the last value.' % arg_content[0], SyntaxWarning) - TMatrix_paths[arg_content[0]] = arg_content[3] - - else: - raise ValueError("--particle expects 3 or 4 arguments, %d given: " % len(arg_content), arg_content) - elif arg_type == 'TMatrix_path': # --TMatrix option - if len(arg_content) == 1: # --TMatrix default_path - if default_TMatrix_path is not None: - warnings.warn('Default T-matrix path already specified. Overriding with the last value.', SyntaxWarning) - default_TMatrix_path = arg_content[0] - elif len(arg_content) > 1: # --TMatrix label [label2 [...]] path - for label in arg_content[:-1]: - if label in TMatrix_paths.keys(): - warnings.warn('T-matrix path for particle \'%s\' already specified.' - 'Overriding with the last value.' % label, SyntaxWarning) - TMatrix_paths[label] = arg_content[-1] - elif arg_type == 'lMax': # --lMax option - if len(arg_content) == 1: # --lMax default_lmax_override - if default_lMax_override is not None: - warnings.warn('Default lMax override value already specified. Overriding the last value.', SyntaxWarning) - default_lMax_override = int(arg_content[-1]) - else: - for label in arg_content[:-1]: - if label in lMax_overrides.keys: - warnings.warn('lMax override for particle \'%s\' already specified.' - 'overriding with the last value.' % label, SyntaxWarning) - lMax_overrides[label] = int(arg_content[-1]) - else: assert False, 'unknown option type' -# Check the info from positions and TMatrix_paths and lMax_overrides -if not set(TMatrix_paths.keys()) <= set(positions.keys()): - raise ValueError("T-Matrix path(s) for particle(s) labeled %s was given, but not their positions" - % str(set(TMatrix_paths.keys()) - set(positions.keys()))) -if not set(lMax_overrides.keys()) <= set(positions.keys()): - raise ValueError("lMax override(s) for particle(s) labeled %s was given, but not their positions" - %str(set(lMax_overrides.keys()) - set(positions.keys()))) -if (set(TMatrix_paths.keys()) != set(positions.keys())) and default_TMatrix_path is None: - raise ValueError("Position(s) of particles(s) labeled %s was given without their T-matrix" - " and no default T-matrix was specified" - % str(set(positions.keys()) - set(TMatrix_paths_keys()))) -for path in TMatrix_paths.values(): - if not os.path.exists(path): - raise ValueError("Cannot access T-matrix file %s. Does it exist?" % path) - -# Assign (pre-parse) the T-matrix operations to individual particles -ops = dict() -for label in positions.keys(): ops[label] = list() -for optype, arg_content in pargs.ops: - # if, no label given, apply to all, otherwise on the specifield particles - for label in (positions.keys() if len(arg_content) == 1 else arg_content[:-1]): - try: - ops[label].append((optype, arg_content[-1])) - except KeyError as e: - e.args += 'Specified operation on undefined particle labeled \'%s\'' % label - raise - -print(sys.stderr, "ops: ", ops) #DEBUG - -#### Collect all the info about the particles / their T-matrices into one list #### -# Enumerate and assign all the _different_ T-matrices (without any intelligent group-theory checking, though) -TMatrix_specs = dict((spec, number) - for (number, spec) in enumerate(set( - (lMax_overrides[label] if label in lMax_overrides.keys() else None, - TMatrix_paths[label], - tuple(ops[label])) - for label in positions.keys() - ))) -# particles_specs contains (label, (xpos, ypos), tmspec_index per element) -particles_specs = [(label, positions(label), - TMatrix_specs[(lMax_overrides[label] if label in lMax_overrides.keys() else None, - TMatrix_paths[label], - tuple(ops[label]))] - ) for label in positions.keys()] - -# -----------------finished basic CLI parsing (except for op arguments) ------------------ -from qpms.timetrack import _time_b, _time_e -btime=_time_b(verbose) - -import qpms -import numpy as np -import os, sys, warnings, math -from scipy import interpolate -nx = None -s3 = math.sqrt(3) - - -# specifikace T-matice zde -cdn = c/ math.sqrt(epsilon_b) -TMatrices_orig, freqs_orig, freqs_weirdunits_orig, lMaxTM = qpms.loadScuffTMatrices(TMatrix_file) -lMax = lMaxTM -if pargs.lMax: - lMax = pargs.lMax if pargs.lMax else lMaxTM -my, ny = qpms.get_mn_y(lMax) -nelem = len(my) -if pargs.lMax: #force commandline specified lMax - TMatrices_orig = TMatrices_orig[...,0:nelem,:,0:nelem] - -TMatrices = np.array(np.broadcast_to(TMatrices_orig[:,nx,:,:,:,:],(len(freqs_orig),2,2,nelem,2,nelem)) ) - -#TMatrices[:,:,:,:,:,ny==3] *= factor13inc -#TMatrices[:,:,:,ny==3,:,:] *= factor13scat -xfl = qpms.xflip_tyty(lMax) -yfl = qpms.yflip_tyty(lMax) -zfl = qpms.zflip_tyty(lMax) -c2rot = qpms.apply_matrix_left(qpms.yflip_yy(3),qpms.xflip_yy(3),-1) - -reCN = re.compile('(\d*)C(\d+)') -#TODO C nekonečno - -for op in ops: - if op[0] == 'all': - targets = (0,1) - elif isinstance(op[0],int): - targets = (op[0],) - else: - targets = op[0] - - if op[1] == 'sym': - mCN = reCN.match(op[2]) # Fuck van Rossum for not having assignments inside expressions - if op[2] == 'σ_z': - for t in targets: - TMatrices[:,t] = (TMatrices[:,t] + qpms.apply_ndmatrix_left(zfl,qpms.apply_ndmatrix_left(zfl, TMatrices[:,t], (-4,-3)),(-2,-1)))/2 - elif op[2] == 'σ_y': - for t in targets: - TMatrices[:,t] = (TMatrices[:,t] + qpms.apply_ndmatrix_left(yfl,qpms.apply_ndmatrix_left(yfl, TMatrices[:,t], (-4,-3)),(-2,-1)))/2 - elif op[2] == 'σ_x': - for t in targets: - TMatrices[:,t] = (TMatrices[:,t] + qpms.apply_ndmatrix_left(xfl,qpms.apply_ndmatrix_left(xfl, TMatrices[:,t], (-4,-3)),(-2,-1)))/2 - elif op[2] == 'C2': # special case of the latter - for t in targets: - TMatrices[:,t] = (TMatrices[:,t] + qpms.apply_matrix_left(c2rot,qpms.apply_matrix_left(c2rot, TMatrices[:,t], -3),-1))/2 - elif mCN: - rotN = int(mCN.group(2)) - TMatrix_contribs = np.empty((rotN,TMatrices.shape[0],2,nelem,2,nelem), dtype=np.complex_) - for t in targets: - for i in range(rotN): - rotangle = 2*np.pi*i / rotN - rot = qpms.WignerD_yy_fromvector(lMax,np.array([0,0,rotangle])) - rotinv = qpms.WignerD_yy_fromvector(lMax,np.array([0,0,-rotangle])) - TMatrix_contribs[i] = qpms.apply_matrix_left(rot,qpms.apply_matrix_left(rotinv, TMatrices[:,t], -3),-1) - TMatrices[:,t] = np.sum(TMatrix_contribs, axis=0) / rotN - else: - raise ValueError('\'%d\' is not an implemented symmetry operation' % op[2]) - elif op[1] == 'tr': - mCN = reCN.match(op[2]) # Fuck van Rossum for not having assignments inside expressions - if op[2] == 'σ_z': - for t in targets: - TMatrices[:,t] = qpms.apply_ndmatrix_left(zfl,qpms.apply_ndmatrix_left(zfl, TMatrices[:,t], (-4,-3)),(-2,-1)) - elif op[2] == 'σ_y': - for t in targets: - TMatrices[:,t] = qpms.apply_ndmatrix_left(yfl,qpms.apply_ndmatrix_left(yfl, TMatrices[:,t], (-4,-3)),(-2,-1)) - elif op[2] == 'σ_x': - for t in targets: - TMatrices[:,t] = qpms.apply_ndmatrix_left(xfl,qpms.apply_ndmatrix_left(xfl, TMatrices[:,t], (-4,-3)),(-2,-1)) - elif op[2] == 'C2': - for t in targets: - TMatrices[:,t] = qpms.apply_matrix_left(c2rot,qpms.apply_matrix_left(c2rot, TMatrices[:,t], -3),-1) - elif mCN: - rotN = int(mCN.group(2)) - power = int(mCN.group(1)) if mCN.group(1) else 1 - TMatrix_contribs = np.empty((rotN,TMatrices.shape[0],2,nelem,2,nelem), dtype=np.complex_) - for t in targets: - rotangle = 2*np.pi*power/rotN - rot = qpms.WignerD_yy_fromvector(lMax, np.array([0,0,rotangle])) - rotinv = qpms.WignerD_yy_fromvector(lMax, np.array([0,0,-rotangle])) - TMatrices[:,t] = qpms.apply_matrix_left(rot, qpms.apply_matrix_left(rotinv, TMatrices[:,t], -3),-1) - else: - raise ValueError('\'%d\' is not an implemented T-matrix transformation operation' % op[2]) - elif op[1] == 'copy': - raise # not implemented - elif op[1] == 'mult': - raise # not implemented - elif op[1] == 'multl': - incy = np.full((nelem,), False, dtype=bool) - for incl in op[2][0].split(','): - l = int(incl) - incy += (l == ny) - scaty = np.full((nelem,), False, dtype=bool) - for scatl in op[2][1].split(','): - l = int(scatl) - scaty += (l == ny) - for t in targets: - TMatrices[np.ix_(np.arange(TMatrices.shape[0]),np.array([t]),np.array([0,1]),scaty,np.array([0,1]),incy)] *= float(op[2][2]) - else: - raise #unknown operation; should not happen - -TMatrices_interp = interpolate.interp1d(freqs_orig*interpfreqfactor, TMatrices, axis=0, kind='linear',fill_value="extrapolate") - -klist_full = qpms.generate_trianglepoints(kdensity, v3d=True, include_origin=True)*3*math.pi/(3*kdensity*hexside) -TMatrices_om = TMatrices_interp(freq) - -chunkn = math.ceil(klist_full.shape[0] / chunklen) - -if verbose: - print('Evaluating %d k-points in %d chunks' % (klist_full.shape[0], chunkn), file = sys.stderr) - sys.stderr.flush() - -metadata = np.array({ - 'lMax' : lMax, - 'maxlayer' : maxlayer, - 'gaussianSigma' : gaussianSigma, - 'epsilon_b' : epsilon_b, - 'hexside' : hexside, - 'chunkn' : chunkn, - 'TMatrix_file' : TMatrix_file, - 'ops' : ops, - }) - -for chunki in range(chunkn): - svdout = '%s_%dnm_%.4f_c%03d.npz' % (pargs.output_prefix, hexside/1e-9, eVfreq, chunki) - - klist = klist_full[chunki * chunklen : (chunki + 1) * chunklen] - - svdres = qpms.hexlattice_zsym_getSVD(lMax=lMax, TMatrices_om=TMatrices_om, epsilon_b=epsilon_b, hexside=hexside, maxlayer=maxlayer, - omega=freq, klist=klist, gaussianSigma=gaussianSigma, onlyNmin=False, verbose=verbose) - - #((svUfullTElist, svSfullTElist, svVfullTElist), (svUfullTMlist, svSfullTMlist, svVfullTMlist)) = svdres - - np.savez(svdout, omega = freq, klist = klist, - metadata=metadata, - uTE = svdres[0][0], - vTE = svdres[0][2], - sTE = svdres[0][1], - uTM = svdres[1][0], - vTM = svdres[1][2], - sTM = svdres[1][1], - - ) - svdres=None - - if scp_dest: - if svdout: - subprocess.run(['scp', svdout, scp_dest]) - -_time_e(btime, verbose) -#print(time.strftime("%H.%M:%S",time.gmtime(time.time()-begtime))) diff --git a/misc/iht-saving.py b/misc/iht-saving.py deleted file mode 100644 index 6565502..0000000 --- a/misc/iht-saving.py +++ /dev/null @@ -1,35 +0,0 @@ -import qpms -import numpy as np -from numpy import newaxis as nx -import math -import cmath -import os -from scipy.constants import c, e as eV, hbar -s3 = math.sqrt(3) - -import argparse - -parser = argparse.ArgumentParser() -parser.add_argument("omega") -#parser.add_argument("maxlayer") -args = parser.parse_args() -omega_eV = float(args.omega) - -print(omega_eV) - -epsilon_b = 2.3104 -hexside = 375e-9 -lMax = 3 -maxlayer = 222 -my, ny = qpms.get_mn_y(lMax) -nelem = len(my) - -omega = omega_eV * eV / hbar - -k_0 = omega * math.sqrt(epsilon_b) / c - -output_prefix = '/tmp/diracpoints-newdata2/%d/' % maxlayer - -os.makedirs(output_prefix, exist_ok=True) -qpms.hexlattice_precalc_AB_save(file=output_prefix+str(omega_eV), lMax=lMax, k_hexside=k_0*hexside, - maxlayer=maxlayer, savepointinfo=True) diff --git a/misc/processWfiles.py b/misc/processWfiles.py deleted file mode 100755 index eca9291..0000000 --- a/misc/processWfiles.py +++ /dev/null @@ -1,11 +0,0 @@ -#!/usr/bin/env python3 - -import sys -from qpms import processWfiles_sameKs - -npart = int(sys.argv[1]) -dest = sys.argv[2] -srcs = sys.argv[3:] - -processWfiles_sameKs(srcs, dest, f='d', nparticles=npart) - diff --git a/misc/processWfiles2part.py b/misc/processWfiles2part.py deleted file mode 100755 index 9704ddc..0000000 --- a/misc/processWfiles2part.py +++ /dev/null @@ -1,10 +0,0 @@ -#!/usr/bin/env python3 - -import sys -from qpms import processWfiles_sameKs - -dest = sys.argv[1] -srcs = sys.argv[2:] - -processWfiles_sameKs(srcs, dest, f='d') - diff --git a/misc/processWfiles_sortnames.py b/misc/processWfiles_sortnames.py deleted file mode 100755 index 6169793..0000000 --- a/misc/processWfiles_sortnames.py +++ /dev/null @@ -1,13 +0,0 @@ -#!/usr/bin/env python3 - -import sys -from qpms import processWfiles_sameKs - -npart = int(sys.argv[1]) -dest = sys.argv[2] -srcs = sys.argv[3:] - -srcs_sorted = sorted(srcs, key=float) - -processWfiles_sameKs(srcs_sorted, dest, f='d', nparticles=npart) - diff --git a/misc/riinfo2c.py b/misc/riinfo2c.py deleted file mode 100644 index e6a0010..0000000 --- a/misc/riinfo2c.py +++ /dev/null @@ -1,31 +0,0 @@ -'''INCOMPLETE! This will read read the refractiveindex.info yaml files -and transforms the database into a C source.''' - -import re -import os -try: - from yaml import CLoader as Loader, CDumper as Dumper -except ImportError: - from yaml import Loader, Dumper - -# Right now, we can process only the 'tabulated nk' data -searchfor = '- type: tabulated nk' -searchfor = re.compile(searchfor) - -ridatadir = "/u/46/necadam1/unix/repo/refractiveindex.info-database/database/data" - -nktables = dict() - -def find_files_by_pattern (pattern, dir): - r = re.compile(pattern) - for parent, dnames, fnames in os.walk(ridatadir): - for fname in fnames: - filename = os.path.join(parent, fname) - if os.path.isfile(filename): - with open(filename) as f: - text = f.read() - if r.search(text): - yield ( - - - diff --git a/misc/subroutines-mstm b/misc/subroutines-mstm deleted file mode 100644 index 73dd2b4..0000000 --- a/misc/subroutines-mstm +++ /dev/null @@ -1,85 +0,0 @@ -ricbessel # ricatti-bessel psi -richankes # ricatti-hankel xi -cricbessel -crichankel # (same with complex argument) -cspherebessel # spherical Bessel jn(z), yn(z) -vcfunc # vector coupling coefficients C(m,n|k,l|m+k,w), w = |n-l|,...n+l -normalizedlegendre # normalized asssociated legendre functions -rotcoef # Generalized spherical functions -taufunc # vector spherical harmonics, normalized -pifunc # vector spherical harmonics, ? -planewavecoef # regular vswf expansion coefficients for a plane wave -gaussianbeamcoef # regular vsfw expansion for a gaussian beam -sphereplanewavecoef # plane wave expansion coefficients at sphere origins -axialtrancoefrecurrence # axial translation ceifficients -axialtrancoefinit -tranordertest # test to determine convergence of regular vswf addition theorem -atcadd -atcdim -moffset -gentrancoef # calculates the vwh translation coefficients for a general translation from one origin to another -cartosphere # cartesian to spherical coorsinates -eulerrotation # euler rotation of a point specified in cartesian coords -ephicoef -planewavetruncationorder # test to determine max order of vswf expansion of a plane wave at distance r -vwhcalc # calculates the cartesian components of the vswf at position rpos -vwhaxialcalc # svwf calculation for an axial translation -twobytwoinverse # inverse of a 2x2 matrix -transfer - -mpisetup - -module spheredata (lots of declarations!, read all the shit) -(...) - -module miecoefdata -miecoefcalc # calculation of the max order of sphere expansions and storage of mie coefficients -readtmatrix # reads and stores a PARTICLE T matrix -lrmodetran # transformation between lr and te tm basis -mieoa # optically aptive lorenz/mie coefficients -getmiedataall # retrieve the array of mie data -getmiedataone # retrieve mie data for a single sphere -onemiecoeffmult # multiplies coefficients for sphere i by appropriate lm coefficient -multmiecoeffmult # generalized mie coefficient mult -dotproduct # vectorproduct for each rhs element of coefficient array - -module translation -hostconfiguration # calculates lists for identifying host and interior sphere -rottranmtrxsetup # sets up the stored translation matrices and sets other constants -rottranmtrxclear # clear the stored translation matrices -sphereinteraction # the general sphere interaction driver -external_to_external_expansion # outgoing translation operator: a(i) = H(i-j) a(j) -external_to_internal_expansion # -m1_to_the_n # sign flipped for odd degrees -rottranfarfield # far field formula for outgoing vswf translation -farfieldtranslationerror # correction ter for hybrid bcgm solution -rottran # the vectorized rotation translation-rotation operation !!!! -spheregaussianbeamcoef # GB coefficients for sphere-centered expansion, obtained via translation -rotvec # rotation of expansion coefficients amn by euler angles - -module scatprops -tranorders # determinaniot of maximum orders for target-based expansions -amncommonorigin # translation of sphere-based expansions to common target origin -lrsphereqeff # general efficiency factor calculation -qefficiencyfactors # calling routine for efficiency calculation -scatteringmatrix # scattering amplitude sa and matrix sm calculation -s11expansion -fosmcalc # azimuth-averaged scattering matrix -formexpansion # determine the generalized sf expansion for the azimuth-averaged scatt. matrix -ranorientscatmatrix -ranorientscatmatrixcalc - -module nearfield -packcoefficient -unpackcoefficient -nearfieldspherepart # the field at point xg generated by the spheres -nearfieldincidentpart # the incident field at point xg using a regular vswh expansion -nearfieldincidentcoef # reshaped array of incident field coefficients -nearfieldpointcalc # ! -nearfieldgridcalc - -module solver -tmatrixsoln # calculation of T-mat. via solution of interaction eqs for a generalized plane wave expansion -fixedorsoln # solution of interaction exuations for a fixed orientation -cbicgff # hybrid bcgm, using far field translation -cbicg # bcgm iteration solver diff --git a/qpms/argproc.py b/qpms/argproc.py index 21d445c..d7cec6e 100644 --- a/qpms/argproc.py +++ b/qpms/argproc.py @@ -1,5 +1,5 @@ ''' -Common snippets for argument processing in command line scripts; legacy scripts use scripts_common.py instead. +Common snippets for argument processing in command line scripts. ''' import argparse diff --git a/qpms/modules.rst b/qpms/modules.rst deleted file mode 100644 index 2de0a7c..0000000 --- a/qpms/modules.rst +++ /dev/null @@ -1,10 +0,0 @@ -scattering.py: Scattering in finite lattices. -modes2d.py TODO: Modes in infinite lattices. -tmatrices.py TODO: T-matrix creation (loading), (symmetry) operations etc. Perhaps move here some content of qpms_p.py -lattices2d.py IN PROGRESS: Various 2D lattice generation, lattice type recognition and related functions. -hexpoints.py: To be obsoleted by more general lattices2d.py. -scripts_common.py: Argument parsing common to various scripts. -timetrack.py: Auxilliary module for measuring elapsed time. -qpms_c.pyx: Cython wrapper for the c code and some miscellanous functions. -qpms_p.py: Miscellanous functions that have not been moved elsewhere. -legacy.py: Unused code moved from old versions, should not be imported with qpms. To be removed in the end. diff --git a/qpms/scripts_common.py b/qpms/scripts_common.py deleted file mode 100644 index e744800..0000000 --- a/qpms/scripts_common.py +++ /dev/null @@ -1,375 +0,0 @@ -''' -Mostly legacy code; new scripts use mostly argproc.py -''' -import warnings -import argparse -#import sys # for debugging purpose, TODO remove in production -import os # because of path -from .types import TMatrixOp, TMatrixSpec, ParticleSpec, LatticeSpec -import collections - -''' # REMOVE IN PRODUCTION -ParticleSpec = collections.namedtuple('ParticleSpec', ['label', 'position', 'tmatrix_spec']) -TMatrixOp = collections.namedtuple('TMatrixOp', - ['optype', 'content']) -TMatrixSpec = collections.namedtuple('TMatrixSpec', - ['lMax_override', 'tmatrix_path', 'ops']) -''' - -__TODOs__ = ''' - - Checking validity of T-matrix ops (the arguments of --tr, --sym or similar) according to what is implemented - in tmatrices.py. - - Implement a more user-friendly way to define the lattice base vectors and positions of the particles. - cf. https://stackoverflow.com/questions/2371436/evaluating-a-mathematical-expression-in-a-string/2371789 - - low priority: allow to perform some more custom operations on T-Matrix, using some kind of parsing from the previous point - - Autodetect symmetries - -''' - -def make_action_sharedlist(opname, listname): - class opAction(argparse.Action): - def __call__(self, parser, args, values, option_string=None): - if (not hasattr(args, listname)) or getattr(args, listname) is None: - setattr(args, listname, list()) - getattr(args,listname).append((opname, values)) - return opAction - - -def add_argparse_k_output_options(parser): - parser.add_argument('--kdensity', '--k_density', action='store', type=int, nargs='+', default=33, help='Number of k-points per x-axis segment FIXME DESCRIPTION') - parser.add_argument('--bz_coverage', action='store', type=float, default=1., help='Brillouin zone coverage in relative length (default 1 for whole 1. BZ)') - parser.add_argument('--bz_edge_width', action='store', type=float, default=0., help='Width of the more densely covered belt along the 1. BZ edge in relative lengths') - parser.add_argument('--bz_edge_factor', action='store', type=float, default=8., help='Relative density of the belt along the 1. BZ edge w.r.t. k_density (default==8)') - parser.add_argument('--bz_edge_twoside', action='store_true', help='Compute also the parts of the densely covered edge belt outside the 1. BZ') - parser.add_argument('--bz_corner_width', action='store', type=float, default=0., help='Size of the more densely covered subcell along the 1. BZ corners in relative lengths') - parser.add_argument('--bz_corner_factor', action='store', type=float, default=16., help='Relative density of the subcell along the 1. BZ corner w.r.t. k_density (default==16)') - parser.add_argument('--bz_corner_twoside', action='store_true', help='Compute also the parts of the densely covered subcell outside the 1. BZ') - return - -def add_argparse_unitcell_definitions(parser): - #TODO create some user-friendlier way to define lattice vectors, cf. https://stackoverflow.com/questions/2371436/evaluating-a-mathematical-expression-in-a-string/2371789 - parser.add_argument('--lattice_base', nargs=4, action='store', type=float, required=True, help='Lattice basis vectors x1, y1, x2, y2') - parser.add_argument('--particle', '-p', nargs='+', action=make_action_sharedlist('particle', 'particlespec'), help='Particle label, coordinates x,y, and (optionally) path to the T-Matrix.') - parser.add_argument('--TMatrix', '-t', nargs='+', action=make_action_sharedlist('TMatrix_path', 'particlespec'), help='Path to TMatrix file') - parser.add_argument('--background_permittivity', action='store', type=float, default=1., help='Background medium relative permittivity (default 1)') - parser.add_argument('--lMax', action=make_action_sharedlist('lMax', 'particlespec'), nargs='+', help='Override lMax from the TMatrix file') - popgrp=parser.add_argument_group(title='Operations') - popgrp.add_argument('--tr', dest='ops', nargs='+', action=make_action_sharedlist('tr', 'ops'), default=list()) # the default value for dest can be set once - popgrp.add_argument('--sym', dest='ops', nargs='+', action=make_action_sharedlist('sym', 'ops')) - #popgrp.add_argument('--mult', dest='ops', nargs=3, metavar=('INCSPEC', 'SCATSPEC', 'MULTIPLIER'), action=make_action_sharedlist('mult', 'ops')) - #popgrp.add_argument('--multl', dest='ops', nargs=3, metavar=('INCL[,INCL,...]', 'SCATL[,SCATL,...]', 'MULTIPLIER'), action=make_action_sharedlist('multl', 'ops')) - return - -def add_argparse_infinite_lattice_options(parser): - parser.add_argument('--maxlayer', action='store', type=int, default=100, help='How far to sum the lattice points to obtain the dispersion') - parser.add_argument('--gaussian', action='store', type=float, metavar='σ', help='Use a gaussian envelope for weighting the interaction matrix contributions (depending on the distance), measured in unit cell lengths (?) FIxME).') - return - -def add_argparse_output_options(parser): - parser.add_argument('--output_prefix', action='store', required=True, help='Prefix to the npz output (will be appended frequency, hexside and chunkno)') - parser.add_argument('--plot_TMatrix', action='store_true', help='Visualise TMatrix on the first page of the output') - parser.add_argument('--scp_to', action='store', metavar='N', type=str, help='SCP the output files to a given destination') - parser.add_argument('--chunklen', action='store', type=int, default=1000, help='Number of k-points per output file (default 1000)') - return - -def add_argparse_common_options(parser): - parser.add_argument('--eVfreq', action='store', required=True, type=float, help='Frequency in eV') - parser.add_argument('--verbose', '-v', action='count', help='Be verbose (about computation times, mostly)') - parser.add_argument('--frequency_multiplier', action='store', type=float, default=1., help='Multiplies the frequencies in the TMatrix file by a given factor.') - -def arg_preprocess_particles(pargs, d=None, return_tuple=False): - ''' - Nanoparticle position and T-matrix path parsing - - parser: ArgumentParser on which add_argparse_unitcell_definitions() and whose - parse_args() has been called. - - returns a list of ParticleSpec objects - ''' - TMatrix_paths = dict() - lMax_overrides = dict() - default_TMatrix_path = None - default_lMax_override = None - if not any((arg_type == 'particle') for (arg_type, arg_content) in pargs.particlespec): - # no particles positions given: suppose only one per unit cell, in the cell origin - positions = {None: (0.0)} - else: - positions = dict() - for arg_type, arg_content in pargs.particlespec: - if arg_type == 'particle': # --particle option - if 3 <= len(arg_content) <= 4: - try: - positions[arg_content[0]] = (float(arg_content[1]), float(arg_content[2])) - except ValueError as e: - e.args += ("second and third argument of --particle must be valid floats, given: ", arg_content) - raise - if len(arg_content) == 4: - if arg_content[0] in TMatrix_paths: - warnings.warn('T-matrix path for particle \'%s\' already specified.' - 'Overriding with the last value.' % arg_content[0], SyntaxWarning) - TMatrix_paths[arg_content[0]] = arg_content[3] - - else: - raise ValueError("--particle expects 3 or 4 arguments, %d given: " % len(arg_content), arg_content) - elif arg_type == 'TMatrix_path': # --TMatrix option - if len(arg_content) == 1: # --TMatrix default_path - if default_TMatrix_path is not None: - warnings.warn('Default T-matrix path already specified. Overriding with the last value.', SyntaxWarning) - default_TMatrix_path = arg_content[0] - elif len(arg_content) > 1: # --TMatrix label [label2 [...]] path - for label in arg_content[:-1]: - if label in TMatrix_paths.keys(): - warnings.warn('T-matrix path for particle \'%s\' already specified.' - 'Overriding with the last value.' % label, SyntaxWarning) - TMatrix_paths[label] = arg_content[-1] - elif arg_type == 'lMax': # --lMax option - if len(arg_content) == 1: # --lMax default_lmax_override - if default_lMax_override is not None: - warnings.warn('Default lMax override value already specified. Overriding the last value.', SyntaxWarning) - default_lMax_override = int(arg_content[-1]) - else: - for label in arg_content[:-1]: - if label in lMax_overrides.keys: - warnings.warn('lMax override for particle \'%s\' already specified.' - 'overriding with the last value.' % label, SyntaxWarning) - lMax_overrides[label] = int(arg_content[-1]) - else: assert False, 'unknown option type' - # Check the info from positions and TMatrix_paths and lMax_overrides - if not set(TMatrix_paths.keys()) <= set(positions.keys()): - raise ValueError("T-Matrix path(s) for particle(s) labeled %s was given, but not their positions" - % str(set(TMatrix_paths.keys()) - set(positions.keys()))) - if not set(lMax_overrides.keys()) <= set(positions.keys()): - raise ValueError("lMax override(s) for particle(s) labeled %s was given, but not their positions" - %str(set(lMax_overrides.keys()) - set(positions.keys()))) - if (set(TMatrix_paths.keys()) != set(positions.keys())) and default_TMatrix_path is None: - raise ValueError("Position(s) of particles(s) labeled %s was given without their T-matrix" - " and no default T-matrix was specified" - % str(set(positions.keys()) - set(TMatrix_paths.keys()))) - # Fill default_TMatrix_path to those that don't have its own - for label in (set(positions.keys()) - set(TMatrix_paths.keys())): - TMatrix_paths[label] = default_TMatrix_path - for path in TMatrix_paths.values(): - if not os.path.exists(path): - raise ValueError("Cannot access T-matrix file %s. Does it exist?" % path) - - # Assign (pre-parse) the T-matrix operations to individual particles - ops = dict() - for label in positions.keys(): ops[label] = list() - for optype, arg_content in pargs.ops: - # if, no label given, apply to all, otherwise on the specifield particles - for label in (positions.keys() if len(arg_content) == 1 else arg_content[:-1]): - try: - ops[label].append(TMatrixOp(optype, arg_content[-1])) - except KeyError as e: - e.args += 'Specified operation on undefined particle labeled \'%s\'' % label - raise - - #### Collect all the info about the particles / their T-matrices into one list #### - # get rid of the non-unique T-matrix specs (so there is only one instance living - # of each different TMatrixSpec, possibly with multiple references to it - TMatrix_specs = dict((spec, spec) - for spec in (TMatrixSpec( - lMax_overrides[label] if label in lMax_overrides.keys() else None, - TMatrix_paths[label], - tuple(ops[label])) - for label in positions.keys()) - ) - # particles_specs contains (label, (xpos, ypos), tmspec per element) - particles_specs = [ParticleSpec(label, positions[label], - TMatrix_specs[(lMax_overrides[label] if label in lMax_overrides.keys() else None, - TMatrix_paths[label], - tuple(ops[label]))] - ) for label in positions.keys()] - - return particles_specs - -''' -import argparse, re, random, string -import subprocess -from scipy.constants import hbar, e as eV, pi, c -import warnings - -parser = argparse.ArgumentParser() -pargs=parser.parse_args() -print(pargs) - -exit(0) ### - -maxlayer=pargs.maxlayer -#DEL hexside=pargs.hexside -eVfreq = pargs.eVfreq -freq = eVfreq*eV/hbar -verbose=pargs.verbose - -#DEL TMatrix_file = pargs.TMatrix - -epsilon_b = pargs.background_permittivity #2.3104 -gaussianSigma = pargs.gaussian if pargs.gaussian else None # hexside * 222 / 7 -interpfreqfactor = pargs.frequency_multiplier -scp_dest = pargs.scp_to if pargs.scp_to else None -kdensity = pargs.kdensity -chunklen = pargs.chunklen - -# -----------------finished basic CLI parsing (except for op arguments) ------------------ -from qpms.timetrack import _time_b, _time_e -btime=_time_b(verbose) - -import qpms -import numpy as np -import os, sys, warnings, math -from scipy import interpolate -nx = None -s3 = math.sqrt(3) - - -# specifikace T-matice zde -cdn = c/ math.sqrt(epsilon_b) -TMatrices_orig, freqs_orig, freqs_weirdunits_orig, lMaxTM = qpms.loadScuffTMatrices(TMatrix_file) -lMax = lMaxTM -if pargs.lMax: - lMax = pargs.lMax if pargs.lMax else lMaxTM -my, ny = qpms.get_mn_y(lMax) -nelem = len(my) -if pargs.lMax: #force commandline specified lMax - TMatrices_orig = TMatrices_orig[...,0:nelem,:,0:nelem] - -TMatrices = np.array(np.broadcast_to(TMatrices_orig[:,nx,:,:,:,:],(len(freqs_orig),2,2,nelem,2,nelem)) ) - -#TMatrices[:,:,:,:,:,ny==3] *= factor13inc -#TMatrices[:,:,:,ny==3,:,:] *= factor13scat -xfl = qpms.xflip_tyty(lMax) -yfl = qpms.yflip_tyty(lMax) -zfl = qpms.zflip_tyty(lMax) -c2rot = qpms.apply_matrix_left(qpms.yflip_yy(3),qpms.xflip_yy(3),-1) - -reCN = re.compile('(\d*)C(\d+)') -#TODO C nekonečno - -for op in ops: - if op[0] == 'all': - targets = (0,1) - elif isinstance(op[0],int): - targets = (op[0],) - else: - targets = op[0] - - if op[1] == 'sym': - mCN = reCN.match(op[2]) # Fuck van Rossum for not having assignments inside expressions - if op[2] == 'σ_z': - for t in targets: - TMatrices[:,t] = (TMatrices[:,t] + qpms.apply_ndmatrix_left(zfl,qpms.apply_ndmatrix_left(zfl, TMatrices[:,t], (-4,-3)),(-2,-1)))/2 - elif op[2] == 'σ_y': - for t in targets: - TMatrices[:,t] = (TMatrices[:,t] + qpms.apply_ndmatrix_left(yfl,qpms.apply_ndmatrix_left(yfl, TMatrices[:,t], (-4,-3)),(-2,-1)))/2 - elif op[2] == 'σ_x': - for t in targets: - TMatrices[:,t] = (TMatrices[:,t] + qpms.apply_ndmatrix_left(xfl,qpms.apply_ndmatrix_left(xfl, TMatrices[:,t], (-4,-3)),(-2,-1)))/2 - elif op[2] == 'C2': # special case of the latter - for t in targets: - TMatrices[:,t] = (TMatrices[:,t] + qpms.apply_matrix_left(c2rot,qpms.apply_matrix_left(c2rot, TMatrices[:,t], -3),-1))/2 - elif mCN: - rotN = int(mCN.group(2)) - TMatrix_contribs = np.empty((rotN,TMatrices.shape[0],2,nelem,2,nelem), dtype=np.complex_) - for t in targets: - for i in range(rotN): - rotangle = 2*np.pi*i / rotN - rot = qpms.WignerD_yy_fromvector(lMax,np.array([0,0,rotangle])) - rotinv = qpms.WignerD_yy_fromvector(lMax,np.array([0,0,-rotangle])) - TMatrix_contribs[i] = qpms.apply_matrix_left(rot,qpms.apply_matrix_left(rotinv, TMatrices[:,t], -3),-1) - TMatrices[:,t] = np.sum(TMatrix_contribs, axis=0) / rotN - else: - raise ValueError('\'%d\' is not an implemented symmetry operation' % op[2]) - elif op[1] == 'tr': - mCN = reCN.match(op[2]) # Fuck van Rossum for not having assignments inside expressions - if op[2] == 'σ_z': - for t in targets: - TMatrices[:,t] = qpms.apply_ndmatrix_left(zfl,qpms.apply_ndmatrix_left(zfl, TMatrices[:,t], (-4,-3)),(-2,-1)) - elif op[2] == 'σ_y': - for t in targets: - TMatrices[:,t] = qpms.apply_ndmatrix_left(yfl,qpms.apply_ndmatrix_left(yfl, TMatrices[:,t], (-4,-3)),(-2,-1)) - elif op[2] == 'σ_x': - for t in targets: - TMatrices[:,t] = qpms.apply_ndmatrix_left(xfl,qpms.apply_ndmatrix_left(xfl, TMatrices[:,t], (-4,-3)),(-2,-1)) - elif op[2] == 'C2': - for t in targets: - TMatrices[:,t] = qpms.apply_matrix_left(c2rot,qpms.apply_matrix_left(c2rot, TMatrices[:,t], -3),-1) - elif mCN: - rotN = int(mCN.group(2)) - power = int(mCN.group(1)) if mCN.group(1) else 1 - TMatrix_contribs = np.empty((rotN,TMatrices.shape[0],2,nelem,2,nelem), dtype=np.complex_) - for t in targets: - rotangle = 2*np.pi*power/rotN - rot = qpms.WignerD_yy_fromvector(lMax, np.array([0,0,rotangle])) - rotinv = qpms.WignerD_yy_fromvector(lMax, np.array([0,0,-rotangle])) - TMatrices[:,t] = qpms.apply_matrix_left(rot, qpms.apply_matrix_left(rotinv, TMatrices[:,t], -3),-1) - else: - raise ValueError('\'%d\' is not an implemented T-matrix transformation operation' % op[2]) - elif op[1] == 'copy': - raise # not implemented - elif op[1] == 'mult': - raise # not implemented - elif op[1] == 'multl': - incy = np.full((nelem,), False, dtype=bool) - for incl in op[2][0].split(','): - l = int(incl) - incy += (l == ny) - scaty = np.full((nelem,), False, dtype=bool) - for scatl in op[2][1].split(','): - l = int(scatl) - scaty += (l == ny) - for t in targets: - TMatrices[np.ix_(np.arange(TMatrices.shape[0]),np.array([t]),np.array([0,1]),scaty,np.array([0,1]),incy)] *= float(op[2][2]) - else: - raise #unknown operation; should not happen - -TMatrices_interp = interpolate.interp1d(freqs_orig*interpfreqfactor, TMatrices, axis=0, kind='linear',fill_value="extrapolate") - -klist_full = qpms.generate_trianglepoints(kdensity, v3d=True, include_origin=True)*3*math.pi/(3*kdensity*hexside) -TMatrices_om = TMatrices_interp(freq) - -chunkn = math.ceil(klist_full.shape[0] / chunklen) - -if verbose: - print('Evaluating %d k-points in %d chunks' % (klist_full.shape[0], chunkn), file = sys.stderr) - sys.stderr.flush() - -metadata = np.array({ - 'lMax' : lMax, - 'maxlayer' : maxlayer, - 'gaussianSigma' : gaussianSigma, - 'epsilon_b' : epsilon_b, - 'hexside' : hexside, - 'chunkn' : chunkn, - 'TMatrix_file' : TMatrix_file, - 'ops' : ops, - }) - -for chunki in range(chunkn): - svdout = '%s_%dnm_%.4f_c%03d.npz' % (pargs.output_prefix, hexside/1e-9, eVfreq, chunki) - - klist = klist_full[chunki * chunklen : (chunki + 1) * chunklen] - - svdres = qpms.hexlattice_zsym_getSVD(lMax=lMax, TMatrices_om=TMatrices_om, epsilon_b=epsilon_b, hexside=hexside, maxlayer=maxlayer, - omega=freq, klist=klist, gaussianSigma=gaussianSigma, onlyNmin=False, verbose=verbose) - - #((svUfullTElist, svSfullTElist, svVfullTElist), (svUfullTMlist, svSfullTMlist, svVfullTMlist)) = svdres - - np.savez(svdout, omega = freq, klist = klist, - metadata=metadata, - uTE = svdres[0][0], - vTE = svdres[0][2], - sTE = svdres[0][1], - uTM = svdres[1][0], - vTM = svdres[1][2], - sTM = svdres[1][1], - - ) - svdres=None - - if scp_dest: - if svdout: - subprocess.run(['scp', svdout, scp_dest]) - -_time_e(btime, verbose) -#print(time.strftime("%H.%M:%S",time.gmtime(time.time()-begtime))) -''' diff --git a/qpms/timetrack.py b/qpms/timetrack.py deleted file mode 100644 index 89364bd..0000000 --- a/qpms/timetrack.py +++ /dev/null @@ -1,35 +0,0 @@ -""" -Legacy code, used only in scripts_common.py. To be removed in future versions. -""" -import time -import sys - -def _time_b(active = True, name = None, step = None): - ''' - Auxiliary function for keeping track of elapsed time. - Returns current time (to be used by _time_e). - ''' - now = time.time() - if active: - if not name: - name = sys._getframe(1).f_code.co_name - if step: - print('%.4f: %s in function %s started.' % (now, step, name), file = sys.stderr) - else: - print('%.4f: Function %s started.' % (now, name), file=sys.stderr) - sys.stderr.flush() - return now - -def _time_e(start_time, active = True, name = None, step = None): - now = time.time() - if active: - if not name: - name = sys._getframe(1).f_code.co_name - if step: - print('%.4f: %s in function %s finished (elapsed %.2f s).' - % (now, step, name, now - start_time), file = sys.stderr) - else: - print('%.4f: Function %s finished (elapsed %.2f s).' - % (now, name, now - start_time), file = sys.stderr) - sys.stderr.flush() -