Dispersion SVD universal script with nice argparsing

Former-commit-id: 613a092eb1dcbcf938e2777736a8758b1a7a6292
This commit is contained in:
Marek Nečada 2017-02-15 21:43:00 +00:00
parent 3e7af7d25e
commit 706701f9ce
1 changed files with 125 additions and 74 deletions

View File

@ -1,37 +1,92 @@
#!/usr/bin/env python3
# coding: utf-8
# In[1]: import argparse
from scipy.constants import hbar, e as eV, pi, c
import random
translations_dir = '/l/necadam1/translations-precalc/diracpoints-newdata/222' def make_action_sharedlist(opname, listname):
TMatrix_file ='/m/home/home4/46/necadam1/unix/tmatrix-experiments/twisted_triangle/silver/twisted_triangle.TMatrix.nonan' 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
pdfout = '/m/home/home4/46/necadam1/unix/tmp/pdf_out/inv-2-mag10-10.pdf' parser = argparse.ArgumentParser()
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('--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', help='Skip frequencies above this value')
parser.add_argument('--eVmin', action='store', 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')
#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('--tr', dest='ops', action=make_action_sharedlist('tr', 'ops'))
parser.add_argument('--tr0', dest='ops', action=make_action_sharedlist('tr0', 'ops'))
parser.add_argument('--tr1', dest='ops', action=make_action_sharedlist('tr1', 'ops'))
parser.add_argument('--sym', dest='ops', action=make_action_sharedlist('sym', 'ops'))
parser.add_argument('--sym0', dest='ops', action=make_action_sharedlist('sym0', 'ops'))
parser.add_argument('--sym1', dest='ops', action=make_action_sharedlist('sym1', 'ops'))
#parser.add_argument('--mult', dest='ops', nargs='2', action=make_action_sharedlist('mult', 'ops'))
#parser.add_argument('--mult0', dest='ops', nargs='2', action=make_action_sharedlist('mult0', 'ops'))
#parser.add_argument('--mult1', dest='ops', nargs='2', action=make_action_sharedlist('mult1', '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)
hexside = 375e-9
epsilon_b = 2.3104
gaussianSigma = None # hexside * 222 / 7
factor13inc = 10 translations_dir = pargs.griddir
factor13scat=10 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)
ops = ( hexside = pargs.hexside #375e-9
# co, typ operace (symetrizace / transformace / kopie), specifikace (operace nebo zdroj), epsilon_b = pargs.background_permittivity #2.3104
# co: 0, 1, (0,1), (0,), (1,), #NI: 'all' gaussianSigma = pargs.gaussian if pargs.gaussian else None # hexside * 222 / 7
# typ operace: sym, tr, copy interpfreqfactor = pargs.frequency_multiplier
# specifikace: kdensity = pargs.kdensity
# sym, tr: 'σ_z', 'σ_y', 'C2'; sym: 'C3', minfreq = pargs.eVmin*eV/hbar if pargs.eVmin else None
# copy: 0, 1 (zdroj) maxfreq = pargs.eVmax*eV/hbar if pargs.eVmax else None
((0,1), 'sym', 'σ_z'), skipfreq = pargs.sparse if pargs.sparse else None
#((0,1), 'sym', 'σ_x'),
#((0,1), 'sym', 'σ_y'),
((0,1), 'sym', 'C3'),
((1), 'tr', 'C2'),
) # TODO multiplier operation definitions and parsing
#factor13inc = 10
#factor13scat=10
interpfreqfactor = 0.5 ops = list()
opre = re.compile('(tr|sym|copy|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()
import qpms import qpms
import numpy as np import numpy as np
@ -40,23 +95,14 @@ import warnings
import math import math
from matplotlib import pyplot as plt from matplotlib import pyplot as plt
from matplotlib.backends.backend_pdf import PdfPages from matplotlib.backends.backend_pdf import PdfPages
from scipy.constants import hbar, e as eV, pi, c
from scipy import interpolate from scipy import interpolate
nx = None nx = None
s3 = math.sqrt(3) s3 = math.sqrt(3)
pdf = PdfPages(pdfout) pdf = PdfPages(pdfout)
# In[2]:
#TODO později
#import argparse
#parser = argparse.ArgumentParser()
#parser.add_argument('--sym', 'mz', 'my', 'mx', 'C3', 'C2' type=str, help='symmetrize both particles')
#args = parser.parse_args()
# In[3]: # In[3]:
# specifikace T-matice zde # specifikace T-matice zde
@ -82,13 +128,16 @@ 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 = np.array(np.broadcast_to(TMatrices_orig[:,nx,:,:,:,:],(len(freqs_orig),2,2,nelem,2,nelem)) )
TMatrices[:,:,:,:,:,ny==3] *= factor13inc #TMatrices[:,:,:,:,:,ny==3] *= factor13inc
TMatrices[:,:,:,ny==3,:,:] *= factor13scat #TMatrices[:,:,:,ny==3,:,:] *= factor13scat
xfl = qpms.xflip_tyty(lMax) xfl = qpms.xflip_tyty(lMax)
yfl = qpms.yflip_tyty(lMax) yfl = qpms.yflip_tyty(lMax)
zfl = qpms.zflip_tyty(lMax) zfl = qpms.zflip_tyty(lMax)
c2rot = qpms.apply_matrix_left(qpms.yflip_yy(3),qpms.xflip_yy(3),-1) 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: for op in ops:
if op[0] == 'all': if op[0] == 'all':
targets = (0,1) targets = (0,1)
@ -98,6 +147,7 @@ for op in ops:
targets = op[0] targets = op[0]
if op[1] == 'sym': if op[1] == 'sym':
mCN = reCN.match(op[2]) # Fuck van Rossum for not having assignments inside expressions
if op[2] == 'σ_z': if op[2] == 'σ_z':
for t in targets: 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 TMatrices[:,t] = (TMatrices[:,t] + qpms.apply_ndmatrix_left(zfl,qpms.apply_ndmatrix_left(zfl, TMatrices[:,t], (-4,-3)),(-2,-1)))/2
@ -107,8 +157,11 @@ for op in ops:
elif op[2] == 'σ_x': elif op[2] == 'σ_x':
for t in targets: 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 TMatrices[:,t] = (TMatrices[:,t] + qpms.apply_ndmatrix_left(xfl,qpms.apply_ndmatrix_left(xfl, TMatrices[:,t], (-4,-3)),(-2,-1)))/2
elif op[2] == 'C3': # FIXME fuj fuj fuj, použij regex!!! elif op[2] == 'C2': # special case of the latter
rotN = 3 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_) TMatrix_contribs = np.empty((rotN,TMatrices.shape[0],2,nelem,2,nelem), dtype=np.complex_)
for t in targets: for t in targets:
for i in range(rotN): for i in range(rotN):
@ -117,12 +170,10 @@ for op in ops:
rotinv = 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) 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 TMatrices[:,t] = np.sum(TMatrix_contribs, axis=0) / rotN
elif op[2] == 'C2':
for t in targets:
TMatrices[:,t] = (TMatrices[:,t] + qpms.apply_matrix_left(c2rot,qpms.apply_matrix_left(c2rot, TMatrices[:,t], -3),-1))/2
else: else:
raise raise
elif op[1] == 'tr': elif op[1] == 'tr':
mCN = reCN.match(op[2]) # Fuck van Rossum for not having assignments inside expressions
if op[2] == 'σ_z': if op[2] == 'σ_z':
for t in targets: for t in targets:
TMatrices[:,t] = qpms.apply_ndmatrix_left(zfl,qpms.apply_ndmatrix_left(zfl, TMatrices[:,t], (-4,-3)),(-2,-1)) TMatrices[:,t] = qpms.apply_ndmatrix_left(zfl,qpms.apply_ndmatrix_left(zfl, TMatrices[:,t], (-4,-3)),(-2,-1))
@ -132,22 +183,24 @@ for op in ops:
elif op[2] == 'σ_x': elif op[2] == 'σ_x':
for t in targets: for t in targets:
TMatrices[:,t] = qpms.apply_ndmatrix_left(xfl,qpms.apply_ndmatrix_left(xfl, TMatrices[:,t], (-4,-3)),(-2,-1)) TMatrices[:,t] = qpms.apply_ndmatrix_left(xfl,qpms.apply_ndmatrix_left(xfl, TMatrices[:,t], (-4,-3)),(-2,-1))
elif op[2] == 'C3': # TODO use regex and generalize
rotN = 3
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)
elif op[2] == 'C2': elif op[2] == 'C2':
for t in targets: for t in targets:
TMatrices[:,t] = qpms.apply_matrix_left(c2rot,qpms.apply_matrix_left(c2rot, TMatrices[:,t], -3),-1) 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': elif op[1] == 'copy':
raise raise # not implemented
else: else:
raise raise #unknown operation; should not happen
TMatrices_interp = interpolate.interp1d(freqs_orig*interpfreqfactor, TMatrices, axis=0, kind='linear',fill_value="extrapolate") TMatrices_interp = interpolate.interp1d(freqs_orig*interpfreqfactor, TMatrices, axis=0, kind='linear',fill_value="extrapolate")
@ -159,7 +212,7 @@ 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)) TMatrix0ip = np.reshape(TMatrices_interp(om)[:,0], (len(om), 2*nelem*2*nelem))
f, axa = plt.subplots(2, 2, figsize=(15,15)) f, axa = plt.subplots(2, 2, figsize=(15,15))
print(TMatrices.shape) #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--')) #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] ax = axa[0,0]
@ -182,21 +235,24 @@ ax2.set_xlim([ax.get_xlim()[0]/eV*hbar,ax.get_xlim()[1]/eV*hbar])
ax.plot( ax.plot(
om, np.unwrap(np.angle(TMatrix0ip[:,:]),axis=0),'-' 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) pdf.savefig(f)
# In[ ]: # In[ ]:
kdensity = 66 #kdensity = 66 #defined from cl arguments
bz_0 = np.array((0,0,0.,)) bz_0 = np.array((0,0,0.,))
bz_K1 = np.array((1.,0,0))*4*np.pi/3/hexside/s3 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_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 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/5)[:,nx] 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] 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] 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/5)[:,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/5)[:,nx] kK2Mlist = bz_K2 + (bz_M-bz_K2) * np.linspace(0,1,kdensity)[:,nx]
B1 = 2* bz_K1 - bz_K2 B1 = 2* bz_K1 - bz_K2
B2 = 2* bz_K2 - bz_K1 B2 = 2* bz_K2 - bz_K1
klist = np.concatenate((k0Mlist,kMK1list,kK10list,k0K2list,kK2Mlist), axis=0) klist = np.concatenate((k0Mlist,kMK1list,kK10list,k0K2list,kK2Mlist), axis=0)
@ -216,11 +272,13 @@ omegalist = list()
filecount = 0 filecount = 0
for trfile in os.scandir(translations_dir): for trfile in os.scandir(translations_dir):
filecount += 1 filecount += 1
if (skipfreq and (0 == filecount % skipfreq)):
continue
try: try:
npz = np.load(trfile.path, mmap_mode='r') npz = np.load(trfile.path, mmap_mode='r')
k_0 = npz['precalc_params'][()]['k_hexside'] / hexside k_0 = npz['precalc_params'][()]['k_hexside'] / hexside
omega = k_0 * c / math.sqrt(epsilon_b) omega = k_0 * c / math.sqrt(epsilon_b)
if(omega < 2.4e15 or omega > 2.7e15 ): if((minfreq and omega < minfreq) or (maxfreq and omega > maxfreq)):
continue continue
except: except:
print ("Unexpected error, trying to continue with another file:", sys.exc_info()[0]) print ("Unexpected error, trying to continue with another file:", sys.exc_info()[0])
@ -314,6 +372,12 @@ for trfile in os.scandir(translations_dir):
minsvTElistarr = np.array(minsvTElistlist) minsvTElistarr = np.array(minsvTElistlist)
minsvTMlistarr = np.array(minsvTMlistlist) minsvTMlistarr = np.array(minsvTMlistlist)
omegalist = np.array(omegalist) omegalist = np.array(omegalist)
# order to make the scatter plots "nice"
omegaorder = np.argsort(omegalist)
omegalist = omegalist[omegaorder]
minsvTElistarr = minsvTElistarr[omegaorder]
minsvTMlistarr = minsvTMlistarr[omegaorder]
omlist = np.broadcast_to(omegalist[:,nx], minsvTElistarr.shape) omlist = np.broadcast_to(omegalist[:,nx], minsvTElistarr.shape)
kxmlarr = np.broadcast_to(kxmaplist[nx,:], minsvTElistarr.shape) kxmlarr = np.broadcast_to(kxmaplist[nx,:], minsvTElistarr.shape)
klist = np.concatenate((k0Mlist,kMK1list,kK10list,k0K2list,kK2Mlist), axis=0) klist = np.concatenate((k0Mlist,kMK1list,kK10list,k0K2list,kK2Mlist), axis=0)
@ -385,19 +449,6 @@ ax.set_xticklabels(['Γ', 'M', 'K', 'Γ', 'K\'','M'])
f.colorbar(sc) f.colorbar(sc)
pdf.savefig(f) pdf.savefig(f)
# In[ ]:
pdf.close() pdf.close()
print(time.strftime("%H.%M:%S",time.gmtime(time.time()-begtime)))
# In[ ]:
unitcell_translations
# In[ ]: