Jdu do práce

Former-commit-id: 78742e79ad31d8aa44ac410401c6b5d6a394a188
This commit is contained in:
Marek Nečada 2017-07-11 06:17:59 +00:00
parent 5249978f45
commit e2f9923f31
2 changed files with 347 additions and 1 deletions

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@ -88,7 +88,7 @@ def range2D(maxN, mini=1, minj=0, minN = 0):
for i in range(mini, maxn + 1): for i in range(mini, maxn + 1):
yield (i, maxn - i) yield (i, maxn - i)
def cellWignerSeitz(b1, b2,): def cellCornersWS(b1, b2,):
""" """
Given basis vectors, returns the corners of the Wigner-Seitz unit cell Given basis vectors, returns the corners of the Wigner-Seitz unit cell
(w1, w2, -w1, w2) for rectangular and square lattice or (w1, w2, -w1, w2) for rectangular and square lattice or

346
qpms/scripts_common.py Normal file
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@ -0,0 +1,346 @@
import argparse
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, 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.')
__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
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
#### 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)))