Jdu do práce

Former-commit-id: 78742e79ad31d8aa44ac410401c6b5d6a394a188

qpms/lattices2d.py

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

qpms/scripts_common.py

@@ -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)))