From 71d1c6f6b1661b85c2423e3818f21b462a579ef8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marek=20Ne=C4=8Dada?= Date: Wed, 28 Jun 2017 15:49:38 +0300 Subject: [PATCH] Starting script for general 2d lattice dispersion Former-commit-id: 7e06a50924e1cdc834aaf519db59bad90380cd09 --- ...ion_chunks.py => dispersion_hex_chunks.py} | 0 misc/generaldisp.py | 239 ++++++++++++++++++ 2 files changed, 239 insertions(+) rename misc/{dispersion_chunks.py => dispersion_hex_chunks.py} (100%) create mode 100755 misc/generaldisp.py diff --git a/misc/dispersion_chunks.py b/misc/dispersion_hex_chunks.py similarity index 100% rename from misc/dispersion_chunks.py rename to misc/dispersion_hex_chunks.py diff --git a/misc/generaldisp.py b/misc/generaldisp.py new file mode 100755 index 0000000..3168c35 --- /dev/null +++ b/misc/generaldisp.py @@ -0,0 +1,239 @@ +#!/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)))