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read_tot_dxplot3.py
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#!/opt/python/2.7.15/gcc-4.8.5/bin/python
import matplotlib
import matplotlib.pyplot as plt
import matplotlib.gridspec as gridspec
import numpy as np
import numpy.ma as ma
import sys, os
import argparse
from hjl_common import *
from basislabel import *
parser = argparse.ArgumentParser(description="Plot ldos with j-basis")
parser.add_argument('ddir', metavar='D', type=str, nargs='+',
help='Data paths' )
parser.add_argument("-s", "--save", action="store_true", help="Only save the fig in .png." )
parser.add_argument("--saveeps", action="store_true", help="Save the fig in .eps too" )
parser.add_argument("--pdf", "--savepdf", action="store_true", help="Save the fig in .pdf too" )
parser.add_argument("--png", action="store_true", help="Save the fig in .png too" )
parser.add_argument("--savetransparent", "--savetp", "--stp", action="store_true", help="Save the fig with transparent background" )
parser.add_argument("--paper", action="store_true" , help="Plot as paper-use." )
parser.add_argument("--fs", "--fermisurface", action="store_true" , help="Plot the fermi-surface." )
parser.add_argument("--oldsoc", action="store_true" , help="SOC strength is in a old-format and multiplied by 2./3." )
parser.add_argument("-l", "--label", type=str, help="set text-label" )
parser.add_argument("--labelcolor", "--lc", type=str, help="specify color of the text-label" )
parser.add_argument("--labelposition", "--lpos", "--labpos", type=float, nargs=2, help="specify position of the text-label" )
parser.add_argument("-y", "--yrange", type=str, help="set yrange e.g. _y0_y1" )
parser.add_argument("-x", "--xxrange", type=str, help="set xrange e.g. _x0_x1" )
parser.add_argument("-z", "--zrange", type=str, help="set zrange e.g. _y0_y1" )
parser.add_argument("--xxrangedos", "--xdos", type=str, help="set xrange e.g. _x0_x1" )
parser.add_argument("--xdatrange", "--xdr", "--xdrange", type=float, nargs=2, help="set xrange and extract e.g. --xdr x0 x1" )
parser.add_argument("--ydatrange", "--ydr", "--ydrange", type=float, nargs=2, help="set xrange and extract e.g. --ydr x0 x1" )
parser.add_argument("-b", "--basis", type=str, help="Set basis. e.g. \"-b j | -b t2g\"" )
parser.add_argument("-c", "--chdat", type=str, help="Choose a component(s) of basis. e.g. \"-c _0_1_2 (default _0_2_4)\"" )
parser.add_argument("--dns", action="store_true", help="Take dataset as down-spin. (setting chdat=[1,3,5])" )
parser.add_argument("-f", "--nofermi", action="store_true", help="Remove the fermi-level line" )
parser.add_argument("--bandpath", type=str, help="Specify the path of band-data.")
parser.add_argument("--band", action="store_true", help="Plot the noninteracting band-data.")
parser.add_argument("--locmax", action="store_true", help="Plot the local maxima together." )
parser.add_argument("--locmaxonly", action="store_true", help="Plot the local maxima only." )
parser.add_argument("--exp", type=str, help="Plot the local maxima only with background of exp data specified" )
parser.add_argument("--th", type=str, help="Set the threshold of local maxima to plot. " )
parser.add_argument("--cb", "--cbar", action="store_true", help="Add the colorbar" )
parser.add_argument("--lineplot", "--lp", type=str, help="Plot along a specfied line. e.g. --lineplot x_0.5" )
parser.add_argument("--lineplotk", "--lpk", action="store_true", help="Plot along the Fermi level in kline(dispersion).")
parser.add_argument("--lineplotkw", "--lpkw", type=str, help="Set the fraction of energy value in the kline-plot, e.g. y_0.51 ." )
parser.add_argument("--lineplotlocmax", "--lplm", type=str, help="Plot along a specfied line. e.g. --lineplotlocmax x_0.5" )
parser.add_argument("--mlineplot", type=str, help="Plot along a specfied line. e.g. --mlineplot x_x0_x1_x2 or y_y1_y2_y3" )
parser.add_argument("--mlineplotlocmax", type=str, help="Plot along a specfied line with locmax. e.g. --mlineplotlocmax x_x0_x1_x2 or y_y1_y2_y3" )
parser.add_argument("--lineplotonly", "--lponly", "--lpo", action="store_true", help="Show the lineplot only" )
parser.add_argument("--lineplotxrange", "--lpx", "--lpxrange", type=str, help="Set x-range of the lineplot" )
parser.add_argument("--lineplotyrange", "--lpy", "--lpyrange", type=str, help="Set y-range of the lineplot" )
parser.add_argument("--lineplotfit", "--lpf", "--lpfit", action="store_true", help="Show fitting of lineplot to the Gaussian.")
parser.add_argument("--noleastsq", "--nolsq", action="store_true", help="Fitting without the least-square method algorithm.")
parser.add_argument("--leastsquare", "--lsq", type=str, help="Change the least-square weight scheme. (default=cauchy) (options=huber,soft_l1,linear)")
parser.add_argument("--readfitparam", "--rfit", "--readfp", action="store_true", help="Read the fitting paramteres from inversetau/tmptauparam.")
parser.add_argument("--savefitparam", "--sfit", "--savefp", action="store_true", help="Save the fitting paramteres in inversetau/tmptauparam.")
parser.add_argument("--grid", action="store_true", help="Take gridspec in mlineplot to plot data separately" )
parser.add_argument("--xgrid", "--xg", "--xgr", action="store_true", help="Take gridspec in mlineplot to plot data separately" )
parser.add_argument("--ygrid", "--yg", "--ygr", action="store_true", help="Take gridspec in mlineplot to plot data separately" )
parser.add_argument("--decomp", action="store_true", help="Plot the basis-decomposed one." )
parser.add_argument("--decompall", action="store_true", help="Plot the all-basis-decomposed one." )
parser.add_argument("--decomponly", action="store_true", help="Plot only impurity-decomposed one without total one." )
parser.add_argument("--decompimp", action="store_true", help="Plot the impurity-decomposed one." )
parser.add_argument("--decompsum", action="store_true", help="Plot the impurity-decomposed one." )
parser.add_argument("--decompsumonly", action="store_true", help="Plot only the impurity-decomposed one." )
parser.add_argument("--decompsumadd", type=str, nargs="+",help="Specify and add other components to the sum, and plot.")
parser.add_argument("--notitle", action="store_true", help="Take no title" )
parser.add_argument("--levhrat", type=float, help="Set the ratio of plotmax- and spectmax-levels." )
parser.add_argument("--levtot", type=str, nargs=3, help="Specify levtot in the false-color plot.")
parser.add_argument("--cptmp", action="store_true", help="Copy the png file to ~/Dropbox/tmp_linux/" )
parser.add_argument("--showaxes", action="store_true", help="Show axes" )
parser.add_argument("--epsilon", "--ep", type=str, help="Set Eipsilon value for different data set" )
parser.add_argument("--epsilontag", "--ept", "--eptag", action="store_true", help="Set Eipsilon tag in file-name." )
parser.add_argument("--epsilontagfloat", "--eptf", "--eptagf", action="store_true", help="Set Eipsilon tag with float number in file-name." )
parser.add_argument("--broadening", "--br", type=str, help="Set Broadening value for different data set" )
parser.add_argument("--broadeningtag", "--brt", "--brtag", action="store_true", help="Set Broadening tag in file-name." )
parser.add_argument("--nof", "--nofermiline", action="store_true", help="Remove the line of Fermi level." )
parser.add_argument("--cmjet", action="store_true", help="Change the color-scheme into plt.cm.jet." )
parser.add_argument("--cm", "--colormap", "--cmap", type=str, help="Specify the color-scheme, e.g. jet of plt.cm.jet." )
parser.add_argument("--cmapnote", "--colormapnote", "--cmnote", action='store_true', help="Specify the color-scheme, e.g. jet of plt.cm.jet." )
parser.add_argument("--proj", "--project", action="store_true", help="Plot the basis-projected spectrum." )
parser.add_argument("--fswn", type=float, help="Set w for FS" )
parser.add_argument("--fswnfloat", "--fswnf", action='store_true', help="Use float-format.")
parser.add_argument("--fsind", type=str, help="Plot a different FS along GX(GV), or with kz-off. e.g. --fsind {vX,vM,or kz0.5}" )
parser.add_argument("--tl", action="store_true", help="Tight-layout" )
parser.add_argument("--count", type=int, help="Set iter")
parser.add_argument("--figs", "--figsize", type=str, help="Set the labels of the legend" )
parser.add_argument("--fontsize", "--fonts", type=str, help="Set the size of fonts.")
parser.add_argument("--legendfontsize", "--lfonts", type=str, help="Set the size of fonts.")
parser.add_argument("--ladjust", "--lad", type=str, help="Set left-adjust value." )
parser.add_argument("--radjust", "--rad", type=str, help="Set right-adjust value." )
parser.add_argument("--badjust", "--bad", type=str, help="Set bottom-adjust value." )
parser.add_argument("--tadjust", "--tad", type=str, help="Set top-adjust value." )
parser.add_argument("--wspace" , "--wsp", type=str, help="Set wspace-adjust value." )
parser.add_argument("--hspace" , "--hsp", type=str, help="Set hspace-adjust value." )
parser.add_argument("--noleg", "--nol", action="store_true", help="Remove the legend.")
parser.add_argument("--leglabel", "--legl", type=str, nargs="+", help="Set the labels of the legend" )
parser.add_argument("--nolab", "--nolabel", action="store_true", help="Remove the xy-label.")
parser.add_argument("--notick", action="store_true", help="Remove ticks." )
parser.add_argument("--noytick", "--noytic", action="store_true", help="Remove y-ticks." )
parser.add_argument("--noxtick", "--noxtic", action="store_true", help="Remove x-ticks." )
parser.add_argument("--noylabel", "--noylab", action="store_true", help="Remove y-label." )
parser.add_argument("--noxlabel", "--noxlab", action="store_true", help="Remove x-label." )
parser.add_argument("--locmaxcolor", "--lmc", "--lmcolor", type=str, help="Set a color of the locmax-plot." )
parser.add_argument("--fermivelocity", "--fermiv", action="store_true", help="Obatina Fermi velocities.")
parser.add_argument("--ldos", "--ld", "--pd", "--pdos", action="store_true", help="Add PDOS as a subplots")
parser.add_argument("--nplot", type=int, help="Set Nplot." )
parser.add_argument("--nplotdos", type=int, help="Set Nplot for dos." )
parser.add_argument("--naxis", type=int, help="Set Naxis." )
parser.add_argument("--nk", "--Nk", type=int, help="Set Nk." )
parser.add_argument("--angle", "--ang", type=str, help="Set kM-kX angle." )
parser.add_argument("--trans", "--tr", action="store_true", help="Transpose the plot" )
parser.add_argument("--yoff", action="store_true", help="Remove xticks." )
parser.add_argument("--dxtick", action="store_true", help="Double the xtick increment." )
parser.add_argument("--dytick", action="store_true", help="Double the ytick increment." )
parser.add_argument("--tickpad", "--tpad", type=str, help="Set pad of tick labels.")
parser.add_argument("--fillb", action="store_true", help="Fill the plotting of blue one." )
parser.add_argument("--sublabel", "--slab", action="store_true", help="Set the labels of sub-figures with alphabet." )
parser.add_argument("--sublabelparameter", "--slabpar", "--slabp", type=str, help="Set a parameter of the sub-labels.")
parser.add_argument("--sublabeloff", "--slaboff", "--slabo", type=str, help="Set the off-set of the sub-labels.")
parser.add_argument("--fermisurfacelabel", "--fslabel", "--fslab", action="store_true", help="Set the labels of fermi-surface." )
parser.add_argument("--fsonly", "--fso", action="store_true", help="Plot fs only.")
parser.add_argument("--fssoc", "--fss", "--osoc", "--onesoc", "--addsoc", "--asoc", type=str, help="Plot the result of the one-shot SOC with specfited strength.")
parser.add_argument("--vertdos", "--vdos", action="store_true", help="Plot DOS in the dispersion from 'vert'.")
parser.add_argument("--vertself", "--vself", action="store_true", help="Plot self-energy in the dispersion from 'vert'.")
parser.add_argument("--vertselfrealpart", "--vselfre", "--vselfreal", action="store_true", help="Plot self-energy in the dispersion from 'vert'.")
parser.add_argument("--nimp", "--ni", "--nimpurity", type=str, help="Set the number of impurity sites.")
args = parser.parse_args()
import matplotlib.pylab as pylab
figs=8.
figsrat = 0.8
figsratpar = 0.25
if args.decomp : figsrat = figsratpar
elif args.decompall : figsrat = figsratpar*2
figsy = figs*figsrat
fsize=10
if args.fontsize : fsize = float( args.fontsize )
fs=fsize
legendfs = fs
if args.legendfontsize : legendfs = float( args.legendfontsize )
ms=figs
if args.figs :
figsarr = args.figs.split("_")
figs = float(figsarr[0])
figsy = float(figsarr[1])
print "figsize = ({}, {})".format( figs, figsy )
def fixfigs() :
if args.figs :
figsarr = args.figs.split("_")
figs = float(figsarr[0])
figsy = float(figsarr[1])
params = { 'legend.fontsize' : legendfs ,
'figure.figsize' : (figs,figsy) ,
'axes.labelsize' : 'x-large' ,
'axes.titlesize' :'small' ,
'xtick.labelsize' :'x-large' ,
'ytick.labelsize' :'x-large' ,
'lines.markersize' : ms ,
#'markers.fillstyle' : 'none' ,
'font.size' : fs }
pylab.rcParams.update(params)
from matplotlib import rc
#rc('font',**{'family':'sans-serif','sans-serif':['Helvetica']})
## for Palatino and other serif fonts use:
#rc('font',**{'family':'serif','serif':['Palatino']})
#rc('text', usetex=True)
ndir = len(args.ddir)
print "ndir : ", ndir
dirarr = args.ddir
i=0
hobjarr = []
for jj in range(ndir) :
print "dir%d:"%i, dirarr[jj] ; i+=1
hobj = headobj( args.ddir[jj] )
hobj.readParameters()
hobjarr.append( hobj )
setattr( hobj, "indZ", 0 )
setattr( hobj, "indZdecomp", 0 )
setattr( hobj, "indZfs", 0 )
setattr( hobj, "indZdecompfs", 0 )
dat = args.ddir[jj]
argsavefigname = dat + "/lattice/vdx/" + hobj.fignamepart()
for ar in sys.argv[1:] :
print "arg : ", ar
if ar.find("Dir")>-1 :
pass
else :
argsavefigname = argsavefigname + '_' + ar.split("-")[-1]
levhrat = 1
if args.levhrat :
levhrat = args.levhrat
if args.notitle : hobj.title = ""
basis = "t2g"
chdat = [0,2,4]
chdat2= [1,0,4]
if args.basis :
basis = args.basis
if basis.find("t")>-1 :
#basis = "t2g"
chdat = [0,2,4]
chdat2= [1,0,4]
if basis.find("j")>-1 :
#basis = "j"
chdat = [1,0,4]
chdat2= [0,2,4]
if basis.find("s")>-1 :
#basis = "s"
chdat = [0,2,3]
chdat2= [1,0,4]
if args.basis.find("z")>-1 :
#basis = basis +"z"
pass
print "basis : ", basis
if args.chdat :
chdat = args.chdat.split("_")
elif args.dns :
chdat = [1,3,5]
epsilon = 0.02
if args.epsilon :
epsilon = float(args.epsilon)
for hobj in hobjarr : hobj.title = hobj.title + " $\eta_s$={}".format(epsilon)
for hobj in hobjarr : setattr( hobj , "epsilon", float(epsilon) )
print "epsilon : ", epsilon
broadening = 0.02
if args.broadening :
broadening = float(args.broadening)
for hobj in hobjarr : hobj.title = hobj.title + " $\eta_d$={}".format(broadening)
for hobj in hobjarr : setattr( hobj , "broadening", float(broadening) )
epsilontag = ""
broadeningtag = ""
if args.epsilontag :
epsilontag = "ep{:g}_".format(epsilon)
if args.epsilontagfloat :
epsilontag = "ep{:.2f}_".format(epsilon)
if args.broadeningtag :
broadeningtag = "br{:g}_".format(broadening)
tagEpBr = epsilontag + broadeningtag
nplot = 1024
if args.nplot : nplot = int(args.nplot)
nax = 1
naxis = 4
if args.naxis : naxis = int(args.naxis)
nktot = 341
if args.nk : nktot = int(args.nk)
angle = False ;
if args.angle : angle = int(args.angle)
def fanglelab(angle) :
if (angle is False) :
return ""
else :
return "_angle{}".format(angle)
anglelab = fanglelab(angle)
angletick = '${}^\circ$'.format(angle)
if args.fswn is not None :
fswn = float( args.fswn )
indfswn = "w{:.2g}".format(fswn)
if args.fswnfloat :
indfswn = "w{:.2f}".format(fswn)
else :
fswn = 0
indfswn = ""
if args.fsind :
if args.fsind.find("kz")>-1 :
fsind = "kz{:g}".format( float(args.fsind[2:]) )
elif args.fsind.find("vX")>-1 or args.fsind.find("vM")>-1 :
fsind = args.fsind
else :
print "ERROR ::'fsind' is not properly given. (args.fsind : ", args.fsind, ")"
sys.exit(1)
else :
fsind = ""
fsfileind = "fs"+fsind+indfswn
if args.broadeningtag :
fsfileind = "fs"+fsind+"w{:g}".format(fswn)
dispfilehead = ""
dispfileind = ""
filehead = ""
if args.fssoc :
filehead = "addsoc{:g}_".format(float(args.fssoc)) + filehead
dispfilehead = "addsoc{:g}_".format(float(args.fssoc)) + dispfilehead
#figs = 12
#fs = 50 ; fsm = 50
cmap = args.cm if args.cm else 'afmhot'
cmapcolor = plt.cm.afmhot # cmapcolor = plt.cm.nipy_spectral
from matplotlib.colors import ListedColormap, LinearSegmentedColormap
if cmap == "jet2" :
ncc = 512
origcolors = plt.cm.get_cmap( 'jet' , ncc )
newcolors = origcolors( np.linspace(0, 1, ncc) )
#print "ORI CORLOR : ", newcolors[:ncc/3,:]
#print "ORI CORLOR : ", newcolors[:ncc/8,:]
#newcolors[:ncc/3,0] = np.sqrt( newcolors[:ncc/3,0] )
#newcolors[:ncc/3,1] = np.sqrt( newcolors[:ncc/3,1] )
#newcolors[:ncc/3,1] = np.sqrt( np.array( np.linspace(0,1,ncc/3) ) )
#newcolors[:ncc/6,0] = np.linspace( 0,1, ncc/6 )
#newcolors[:ncc/12,0] = np.zeros( ncc/12 ) +1
#newcolors[:ncc/12,1] = np.zeros( ncc/12 ) +1
#newcolors[:ncc/12,2] = np.zeros( ncc/12 ) +1
newcolors[:ncc/8,:] = np.power( newcolors[:ncc/8,:] , 2 )
newcolors[:ncc/10,:] = np.power( newcolors[:ncc/10,:] , 2 )
#print "NEW CORLOR : ", newcolors[:ncc/3,:]
cmapcolor = ListedColormap( newcolors )
print "Modifying colormap. Done."
elif cmap == "jet3" :
ncc = 512
origcolors = plt.cm.get_cmap( 'jet' , ncc )
newcolors = origcolors( np.linspace(0, 1, ncc) )
#print "ORI CORLOR : ", newcolors[:ncc/3,:]
nccb = 174
#print "ORI CORLOR : ", newcolors[:ncc/8,:]
#newcolors[:ncc/3,0] = np.sqrt( newcolors[:ncc/3,0] )
#newcolors[:ncc/3,1] = np.sqrt( newcolors[:ncc/3,1] )
#newcolors[:ncc/3,1] = np.sqrt( np.array( np.linspace(0,1,ncc/3) ) )
#newcolors[:ncc/6,0] = np.linspace( 0,1, ncc/6 )
#newcolors[:ncc/12,0] = np.zeros( ncc/12 ) +1
#newcolors[:ncc/12,1] = np.zeros( ncc/12 ) +1
#newcolors[:ncc/12,2] = np.zeros( ncc/12 ) +1
#newcolors[:ncc/8,:] = np.power( newcolors[:ncc/8,:] , 2 )
#newcolors[:ncc/10,:] = np.power( newcolors[:ncc/10,:] , 2 )
newcolors[:nccb,2] = np.linspace(0,1,nccb)
#print "NEW CORLOR : ", newcolors[:ncc/3,:]
cmapcolor = ListedColormap( newcolors )
print "Modifying colormap. Done."
elif cmap == "GreysMid" :
print cmap
origcolors = plt.cm.get_cmap( 'Greys' , 256 )
newcolors = origcolors( np.linspace(0.8, 1, 80) )
newcolorsbottom = origcolors( np.linspace(0, 0.8, 200) )
#newcolorsbottom[:,:] = 1
print "ORI CORLOR bottom : ", newcolorsbottom
newcolors = np.vstack( (newcolorsbottom, newcolors) )
print "NEW CORLOR : ", newcolors
#top = cm.get_cmap('Oranges_r', 128)
#bottom = cm.get_cmap('Blues', 128)
#newcolors = np.vstack((top(np.linspace(0, 1, 128)), bottom(np.linspace(0, 1, 128))))
cmapcolor = ListedColormap( newcolors )
#os.exit(1)
elif args.cmjet :
cmapcolor = plt.cm.jet
elif args.cm :
cmapcolor = getattr( plt.cm , args.cm )
if args.proj :
cmapcolor = [ plt.cm.binary , plt.cm.Reds , plt.cm.Greens , plt.cm.Blues ]
def gaussftn( x, ymax, x0, sigmax ) :
return ymax * sigmax * sigmax / ( (x-x0)*(x-x0) + sigmax*sigmax )
def func( var, t, y ) :
return gaussftn( t, var[0], var[1], var[2] ) + gaussftn( t, var[3], var[4], var[5] ) - y
def funcmirrorpi( var, t, y ) :
return gaussftn( t, var[0], var[1], var[2] ) + gaussftn( t, var[3], var[4], var[5] ) + gaussftn( -t+200./341, var[0], var[1], var[2] ) + gaussftn( -t+200./341, var[3], var[4], var[5] ) - y
def gendata( t, var ) :
return gaussftn( t, var[0], var[1], var[2] ) + gaussftn( t, var[3], var[4], var[5] )
def gendatamirrorpi( t, var ) :
return gaussftn( t, var[0], var[1], var[2] ) + gaussftn( t, var[3], var[4], var[5] ) + gaussftn( -t+200./341, var[0], var[1], var[2] ) + gaussftn( -t+200./341, var[3], var[4], var[5] )
class kline :
def __init__ ( self, fig, cmapcolor , ax=False , findlocmax=False, lev=300 ) :
#count = np.genfromtxt( hobj.ddir + "/parameters_u{:.2f}.dat".format(hobj.UF) , dtype=int )
#try :
# lcount = count.shape[1]
# print "csh : ", count.shape
# count = count[-1][0]
#except IndexError :
# count = count[0]
#fspect = "{}/lattice/vdx/u{:.2f}_ts0.00_d{:.3f}_ep{}_{}th.txt".format( hobj.ddir, hobj.u, hobj.D ,epsilon, hobj.count )
#faxis = "{}/lattice/vdx/naxis4_Nplot1024_Nk341_ep{}_{}th.dx".format( hobj.ddir, epsilon, hobj.count )
nkgrid=[]
print "Entering kline().."
print "1:", faxis
print "2:", fspect
f = open(faxis, "r")
for line in f:
values = line.split()
if "KNAMES" in line:
knames = values[1:]
print knames,
if "KPOINTS" in line:
nkgrid = values[1:]
nkgrid = np.array( nkgrid , dtype=int)
print nkgrid,
if "object 2" in line:
ny = int(values[-2])
nx = int(values[-1])
if "origin" in line:
ori = float(values[-1])
if "delta" in line:
if float(values[-1]) > 0 :
deltay = float(values[-1])
else:
deltax = float(values[-2])
print ""
f.close()
xi = []
yi = []
xi = np.linspace( 0, nx*deltax, nx )
ximax = (nx-1)*deltax
yi = np.linspace( ori, ori+ny*deltay, ny )
ntot = nx*ny
Z=[]
f2= open(fspect, "r")
nbasis = 6
if fspect.find("band_")>-1 :
print "Read", nx, "band data"
Z = range(nx * nbasis)
if "u{:.2f}".format(hobj.u) in fspect :
print "Read", ntot, "density data"
Z = range(ntot)
ncount = 0
ndata = 0
for line in f2 :
values = line.split()
darr = []
for j in range(len(values)) :
Z[ndata] = float(values[j])
#darr.append(float(values[j]))
#Z = np.append( Z, np.array(darr) )
#Z = np.append( Z, np.array([float(values[0]), float(values[1]), float(values[2]), float(values[3]), float(values[4])]) )
#for j in range(5) :
#np.append( Z, float(values[j]) )
#if( j > 5 ) :
#print "ERROR"
ndata += 1
ncount += 1
#print "\rnline={:10d}".format(ncount),
#print "\rnline={:3.1f}%".format(float(ncount)/ntot*100.),
print "nc=", ncount
print "ndata=", ndata
if "u{:.2f}".format(hobj.u) in fspect :
X, Y = np.meshgrid(xi, yi)
Z = np.array(Z)
Z=Z.reshape(X.shape)
self.Z = Z
#if args.xdatrange :
# xmin, xmax = args.xdatrange
# xind = np.bitwise_and( xi>xmin, xi<xmax )
# Xind = np.meshgrid( xind, yi ) [0]
#if args.ydatrange :
# ymin, ymax = args.ydatrange
# yind = np.bitwise_and( yi>ymin, yi<ymax )
# Yind = np.meshgrid( xi, yind ) [1]
#if args.xdatrange or args.ydatrange :
# zind =
#Z = np.ma.array( Z, mask=Z < 1 )
if ax : self.cbar = ax.contourf(X, Y, Z, lev, rstride=1, cstride=1, cmap=cmapcolor, linewidth=0, antialiased=False)
if args.cb :
if args.fs : pass
#elif (args.decomp is not None ) : self.cb = plt.colorbar( self.cbar )
#plt.axis([0,1,-3,6])
if args.yrange :
ymin = float( args.yrange.split("_")[-2] )
ymax = float( args.yrange.split("_")[-1] )
if ax : ax.axis( [0,1,ymin,ymax] )
if ax : axSetRange( ax, args.xxrange , "x" )
textc = args.labelcolor if args.labelcolor else 'k'
if args.label :
if ax : ax.text( 0.8, ymax*1.02, "{}".format( args.label ), color=textc )
if args.leglabel :
textc = args.labelcolor if args.labelcolor else 'k'
textpos = args.labelposition if args.labelposition else [0.1,0.9]
leglabel = ""
sep = ", " if len(args.leglabel)>1 else ""
for leglabelpar in args.leglabel :
leglabelval = "={}".format( getattr( hobj, leglabelpar ) )
if args.paper :
try :
leglabelval = " = {:.3f}".format( float( getattr( hobj, leglabelpar )) )
if leglabelpar == "Treal" :
leglabelval = " = {:.0f}".format( float( getattr( hobj, leglabelpar )) )
except : pass
leglabel += filterlabel(leglabelpar) + leglabelval + sep
if ax : ax.text( textpos[0], textpos[1], leglabel, color=textc, transform=ax.transAxes )
if args.bandpath :
print "Add band"
yb = range(nx * nbasis)
ndata = 0
ncount = 0
with open(args.bandpath) as fband :
f2 = fband.readlines()
for line in f2 :
values = line.split()
darr = []
for j in range(len(values)) :
yb[ndata] = float(values[j])
ndata += 1
ncount += 1
print "\rnline={:10d} in band-data".format(ncount),
#print "\rnline={:3.1f}%".format(float(ncount)/ntot*100.),
yb = np.array(yb)
yb = yb.reshape( (nx,nbasis) )
#print yb
yb = yb.transpose()
for i in range( nbasis ) :
if ax : ax.plot( xi, yb[i], "k:", lw = 0.7)
if fspect.find("band_")>-1 :
X = xi
Z = np.array(Z)
Z = Z.reshape((nx,nbasis))
Z = Z.transpose()
self.Z = Z
print "len x,z =", len(X), len(Z)
for i in range( nbasis ) :
if ax : ax.plot(X, Z[i], "b-")
if ax : ax.axis([0,1,-3,2])
if args.yrange :
ymin = float( args.yrange.split("_")[-2] )
ymax = float( args.yrange.split("_")[-1] )
if ax : ax.axis( [0,1,ymin,ymax] )
if args.label :
textc = args.labelcolor if args.labelcolor else 'k'
if ax : ax.text( 0.8, ymax*1.02, "{}".format( args.label ), color=textc )
if args.leglabel :
textc = args.labelcolor if args.labelcolor else 'k'
textpos = args.labelposition if args.labelposition else [0.1,0.9]
leglabel = ""
sep = ", " if len(args.leglabel)>1 else ""
for leglabelpar in args.leglabel :
leglabelval = "={}".format( getattr( hobj, leglabelpar ) )
if args.paper :
try :
leglabelval = " = {:.3f}".format( float( getattr( hobj, leglabelpar )) )
if leglabelpar == "Treal" :
leglabelval = " = {:.0f}".format( float( getattr( hobj, leglabelpar )) )
except : pass
leglabel += filterlabel(leglabelpar) + leglabelval + sep
if ax : ax.text( textpos[0], textpos[1], leglabel, color=textc, transform=ax.transAxes )
#plt.plot(X, Z[0], X, Z[1], X, Z[2], X, Z[3], X, Z[4], X, Z[5])
#plt.plot(X, Z[0], X, Z[1], 300, rstride=1, cstride=1, cmap=cmapcolor, linewidth=0, antialiased=False)
print "Read", nx, "band data"
#surf = ax.contourf(X, Y, Z, 300, rstride=1, cstride=1, cmap=cm.nipy_spectral, linewidth=0, antialiased=False)
#plt.savefig("{}/lattice/vdx/spect_u{}.png".format(hobj.ddir,u) )
#print "scalex:", scalex
# Fermi level
if args.nofermi : None
else :
dashpt= [1,1]
if ax : ax.axhline( 0, 0,1 , color='w', dashes=dashpt , lw=0.5)
#plt.plot( [0, 0], [1,0], "k-", lw = 1)
nkgridtot = 0
xtics = np.zeros(naxis)
for i in range(len(nkgrid)) :
nkgridtot += nkgrid[i]
xtics[i+1] = nkgridtot
print "KPOINTS, TOTAL : ", xtics, nkgridtot
xtics = xtics / float(nkgridtot)
print "xtics rescaled from KPOINTS/TOTAL : ",
print xtics
print "KNAMES converted : ",
for i in range( len(knames) ) :
if( knames[i].find('G') > -1 ) :
knames[i] = '$\Gamma$'
elif( knames[i].find('a') > -1 ) :
knames[i] = angletick
print knames
if ax : ax.set_xticks(xtics)
if ax : ax.set_xticklabels(knames )
if ax : ax.tick_params( axis='y')
if ax : ax.tick_params( axis='both', direction="in" )
if ax : ax.set_ylabel(r"$E$ [eV]")
if ax : axSetRange( ax, args.xxrange , "x" )
if args.noylabel : ax.set_ylabel('') ; ax.set_yticks([])
#if args.exp :
# #if args.exp.find("B" )>-1 :
# expfig = "/home/jun/Dropbox/tmp_linux/Ref_Shen2007PRL.png"
# img = plt.imread( expfig )
# xG = float(xtics[0])
# xM = float(xtics[1]) #as (Pi,0)
# ax.imshow(img, extent=[xM*0.7,xM,-0.1,0] )
self.X = X
self.Y = Y
self.Z = Z
self.nx = nx
self.ny = ny
self.xtics=xtics
self.knames=knames
if findlocmax :
findLocalMaxSave( Z, "{}/lattice/vdx/".format( hobj.ddir ) , hobj , fhead='disp', XY=[X,Y] )
class klinedecomp :
def __init__( self, ax , bcomp , lev , cmapcolor , Zdat=None , findlocmax=False ) :
print "Entering klinedecomp().."
print "klinedecomp ", bcomp, cmapcolor, lev[0], lev[-1]
count = np.genfromtxt( hobj.ddir + "/parameters_u{:.2f}.dat".format(hobj.UF) , dtype=int )
try :
lcount = count.shape[1]
count = count[lcount-1][0]
except IndexError :
count = count[0]
#for fname in os.listdir( os.getcwd()+'/'+hobj.ddir+"/lattice/vdx/" ) :
# if ".txt" in fname :
# if "decomp" in fname and "_fs_" not in fname :
# fspectdecomp = "{}/lattice/vdx/{}".format( hobj.ddir, fname )
# elif "_fs_" not in fname :
# fspect = "{}/lattice/vdx/{}".format( hobj.ddir, fname )
# if ".dx" in fname :
# if "decomp" in fname and "_fs_" not in fname :
# faxisdecomp = "{}/lattice/vdx/{}".format( hobj.ddir, fname )
# elif "_fs_" not in fname :
# faxis = "{}/lattice/vdx/{}".format( hobj.ddir, fname )
nkgrid=[]
if args.decomp or args.decompall:
faxis = faxisdecomp
fspect = fspectdecomp
faxis = faxisdecomp
fspect = fspectdecomp
print "1:", faxis
print "2:", fspect
f = open(faxis, "r")
for line in f:
values = line.split()
if "KNAMES" in line:
knames = values[1:]
print knames,
if "KPOINTS" in line:
nkgrid = values[1:]
nkgrid = np.array( nkgrid , dtype=int)
print nkgrid,
if "object 2" in line:
self.ny = int(values[-2])
self.nx = int(values[-1])
if "Nx" in line:
self.nx = int(values[1])
if "Ny" in line:
self.ny = int(values[1])
if "origin" in line:
ori = float(values[-1])
if "delta" in line:
if float(values[-1]) > 0 :
deltay = float(values[-1])
else:
deltax = float(values[-2])
if "datafile" in line:
fspect = hobj.ddir + "/lattice/vdx/" + values[1]
if "xrange" in line:
xmin = float( values[1] )
xmax = float( values[2] )
if "yrange" in line:
ymin = float( values[1] )
ymax = float( values[2] )
f.close()
print ""
xi = []
yi = []
try :
xi = np.linspace( xmin, xmax , self.nx )
except :
xi = np.linspace( 0, (self.nx-1)*deltax , self.nx )
ximax = (self.nx-1)*deltax
try :
yi = np.linspace( ymin, ymax , self.ny )
except :
yi = np.linspace( 0, (self.ny-1)*deltay , self.ny )
yimax = (self.ny-1)*deltay
if hobj.indZdecomp :
Z = hobj.Zdecomp
else :
Z= np.genfromtxt( fspect, dtype=float )
hobj.Zdecomp = Z
hobj.indZdecomp = 1
ntot = self.nx*self.ny
nbasis = 6
ncount = len(Z) * len(Z[0])
ndata = len(Z[0])
print "nx,ny,ntot,ncount,nZline,ndata : ", self.nx, self.ny, ntot, ncount, len(Z), ndata,
f2= open(fspect, "r")
nbasis = 6
ni = 1
try : ni = int( hobj.ni )
except : pass
if args.nimp :
ni = int( args.nimp )
if "u{:.2f}".format(hobj.u) in fspect :
print "Z[{}][{}]".format( np.shape(Z)[0], np.shape(Z)[1] ),
#self.Z = [0.]*ntot
ncount = 0
ndata = 0
NU = ni*nbasis
if bcomp > -1 :
if basis.find("j")>-1 or basis.find("z")>-1 :
self.Z = np.array( Z[bcomp] ,dtype=float )
elif basis.find("s")>-1 :
self.Z = np.array( Z[bcomp+NU*2] ,dtype=float )
else :
self.Z = np.array( Z[bcomp+NU] ,dtype=float )
else :
self.Z = Z
ax.axis( [ xi[0],xi[-1], yi[0],yi[-1] ] )
if "u{:.2f}".format(hobj.u) in fspect :
X, Y = np.meshgrid(xi, yi)
self.X = X
self.Y = Y
if Zdat is not None :
Zdatplot = Zdat
self.Z = Zdatplot
else :
self.Z = np.array(self.Z)
self.Z = self.Z.reshape(X.shape)
Zdatplot = self.Z
self.cbar = ax.contourf(X, Y, Zdatplot, lev, rstride=1, cstride=1, cmap=cmapcolor, linewidth=0, antialiased=False)
#if args.cb :
# cb = plt.colorbar( self.cbar )
if args.yrange :
ymin = float( args.yrange.split("_")[-2] )
ymax = float( args.yrange.split("_")[-1] )
ax.axis( [0,1,ymin,ymax] )
if args.label :
textc = args.labelcolor if args.labelcolor else 'k'
ax.text( 0.8, ymax*1.02, "{}".format( args.label ), color=textc )
if args.leglabel :
textc = args.labelcolor if args.labelcolor else 'k'
textpos = args.labelposition if args.labelposition else [0.1,0.9]
leglabel = ""
sep = ", " if len(args.leglabel)>1 else ""
for leglabelpar in args.leglabel :
leglabelval = "={}".format( getattr( hobj, leglabelpar ) )
if args.paper :
try :
leglabelval = " = {:.3f}".format( float( getattr( hobj, leglabelpar )) )
if leglabelpar == "Treal" :
leglabelval = " = {:.0f}".format( float( getattr( hobj, leglabelpar )) )
except : pass
leglabel += filterlabel(leglabelpar) + leglabelval + sep
if ax : ax.text( textpos[0], textpos[1], leglabel, color=textc, transform=ax.transAxes )
#ax.text( 0.8, ymax*1.02, "{}".format( bolabel(basis,bcomp) ) )
if basis.find("t")>-1 : fsrat = 1
else : fsrat=1
if (Zdat is not None) and bcomp==0 :
bcomp -= 1
if bcomp<0 :
lab =''
else :
lab = ''
#lab = r"${}$".format( bolabel(basis,bcomp) )
ax.text( 0.5, ymax*0.8, lab , horizontalalignment='center', va='center', color='w' , size=fsize*fsrat )
dashpt = [1,1]
if args.nof : pass
else : ax.axhline( 0, 0,1, color='w', dashes=dashpt, lw=0.5 )
print "xtics rescaled : ",
nkgridtot = 0
xtics = np.zeros(naxis)
for i in range(len(nkgrid)) :
nkgridtot += nkgrid[i]
xtics[i+1] = nkgridtot
xtics = xtics / float(nkgridtot)
#print nkgrid
print xtics
print "knames converted : ",
for i in range( len(knames) ) :
if( knames[i].find('G') > -1 ) :
knames[i] = '$\Gamma$'
elif( knames[i].find('a') > -1 ) :
knames[i] = angletick
print knames
ax.set_xticks(xtics)
ax.set_xticklabels(knames)
ax.tick_params( axis='y')
ax.tick_params( axis='both', direction="in" )
#ax.set_ylabel(r"$E$ (eV)", fontsize = fs )
if findlocmax :
findLocalMaxSave( Zdatplot, "{}/lattice/vdx/".format( hobj.ddir ) , hobj , fhead='disp', XY=[X,Y] )
class fsurface :
def __init__( self, ax=False ) :
#count = np.genfromtxt( hobj.ddir + "/parameters_u{:.2f}.dat".format(hobj.UF) , dtype=int )
#try :
# lcount = count.shape[1]
# count = count[lcount-1][0]
#except IndexError :
# count = count[0]
#for fname in os.listdir( os.getcwd()+'/'+hobj.ddir+"/lattice/vdx/" ) :
# if "ep{}".format(epsilon) in fname :
# if ".txt" in fname :
# if "decomp" in fname :
# fspectdecomp = "{}/lattice/vdx/{}".format( hobj.ddir, fname )
# else :
# fspect = "{}/lattice/vdx/{}".format( hobj.ddir, fname )
# elif ".dx" in fname :
# if "decomp" in fname :
# faxisdecomp = "{}/lattice/vdx/{}".format( hobj.ddir, fname )
# else :
# faxis = "{}/lattice/vdx/{}".format( hobj.ddir, fname )
print "Entering fsurface().."
nkgrid=[]
print "1:", faxis
print "2:", fspect
f = open(faxis, "r")
for line in f:
values = line.split()
if "KNAMES" in line:
knames = values[1:]
print knames
if "KC" in line:
kc = values[1]
if "KR" in line:
kr = values[1]
if "KPOINTS" in line:
nkgrid = values[1:]
nkgrid = np.array( nkgrid , dtype=int)
print nkgrid
self.ny = int(nkgrid[-1])
self.nx = int(nkgrid[-2])
if "origin" in line:
ori = float(values[-1])
if "delta" in line:
if float(values[-1]) > 0 :
deltay = float(values[-1])
else:
deltax = float(values[-2])
f.close()
xi = []
yi = []
xi = np.linspace( 0, (self.nx-1)*deltax , self.nx )
ximax = (self.nx-1)*deltax
yi = np.linspace( 0, (self.ny-1)*deltay , self.ny )
ntot = self.nx*self.ny
self.Z=[]
f2= open(fspect, "r")
nbasis = 6
if "u{:.2f}".format(hobj.u) in fspect :
print "Read", ntot, "density data"
self.Z = [0.]*ntot
ncount = 0
ndata = 0
for line in f2 :
values = line.split()
darr = []
for j in range(len(values)) :
self.Z[ndata] = float(values[j])
#darr.append(float(values[j]))
#Z = np.append( Z, np.array(darr) )
#Z = np.append( Z, np.array([float(values[0]), float(values[1]), float(values[2]), float(values[3]), float(values[4])]) )
#for j in range(5) :
#np.append( Z, float(values[j]) )
#if( j > 5 ) :
#print "ERROR"
ndata += 1
ncount += 1
print "\rnline={:10d}".format(ncount),
#print "\rnline={:3.1f}%".format(float(ncount)/ntot*100.),
print "nc=", ncount
print "ndata=", ndata
if "u{:.2f}".format(hobj.u) in fspect :
X, Y = np.meshgrid(xi, yi)
self.X = X
self.Y = Y
self.Z = np.array(self.Z) * nbasis*0.5
self.Z =self.Z.reshape(X.shape)
levh = self.Z.max()
lev = np.linspace( 0, levh*levhrat, 300 )
if ax : self.cbar = ax.contourf(X, Y, self.Z, lev, rstride=1, cstride=1, cmap=cmapcolor, linewidth=0, antialiased=False)
if args.cb and (args.decompall is None) and (args.decomp is None) :
plt.colorbar( self.cbar )
if ax : ax.axis('scaled')
if ax : ax.axis([0,1,0,1])
#plt.tight_layout()
try :
if( kc.find('G') > -1 ) : kc = '$\Gamma$'
if( kr.find('G') > -1 ) : kr = '$\Gamma$'
if( knames[0].find('G') > -1 ) : knames[0] = '$\Gamma$'
#fs = 25
fc = 'w'
if args.fermisurfacelabel :
if ax : ax.text( 0.5, 0.5, kc , color=fc , fontsize=fsize , zorder=12 )
if ax : ax.text( 0.88, 0.5, kr , color=fc , fontsize=fsize , zorder=12 )
if args.fs :
if ax : ax.text( 0.88, 0.88, knames[0] , color=fc , fontsize=fsize , zorder=12 )
else :
if ax : ax.text( 1.0, 0.0, knames[0] , color=fc , fontsize=fsize , zorder=12 )
except : pass
if args.notick : pass
else :
if ax : ax.set_xticks([])
if ax : ax.set_xticklabels([])
if ax : ax.set_yticks([])
if ax : ax.set_yticklabels([])
#if args.yrange :
# ymin = float( args.yrange.split("_")[-2] )
# ymax = float( args.yrange.split("_")[-1] )
# ax.axis( [0,1,ymin,ymax] )
if args.label :
textc = args.labelcolor if args.labelcolor else 'k'
if ax : ax.text( 0.8, 1.02, "{}".format( args.label ), color=textc )
if args.leglabel :
textc = args.labelcolor if args.labelcolor else 'k'
textpos = args.labelposition if args.labelposition else [0.1,0.9]
leglabel = ""
sep = ", " if len(args.leglabel)>1 else ""
for leglabelpar in args.leglabel :
leglabelval = "={}".format( getattr( hobj, leglabelpar ) )
if args.paper :
try :
leglabelval = " = {:.3f}".format( float( getattr( hobj, leglabelpar )) )
if leglabelpar == "Treal" :
leglabelval = " = {:.0f}".format( float( getattr( hobj, leglabelpar )) )
except : pass
leglabel += filterlabel(leglabelpar) + leglabelval + sep
if ax : ax.text( textpos[0], textpos[1], leglabel, color=textc, transform=ax.transAxes )
if fswn != 0. :
if ax : ax.text( 0, 1.02, r"$\omega=$"+"{}".format( fswn ) )
#Ztr = self.Z.transpose()
#dztr = Ztr - self.Z
#print "NNZ Z-Z.tr :"
#for ii in range(self.nx) :
# for jj in range(self.nx) :
# if dztr[ii][jj] > 1e-6 :
# print "({}\t{})".format(ii,jj)
findLocalMaxSave( self.Z, "{}/lattice/vdx/".format( hobj.ddir ) , hobj )
class fsurfacedecomp :
def __init__( self, ax , bcomp , lev , Zdat=None , findlocmax=False) :
print "Entering fsurfacedecomp().."
count = np.genfromtxt( hobj.ddir + "/parameters_u{:.2f}.dat".format(hobj.UF) , dtype=int )
try :
lcount = count.shape[1]
count = count[lcount-1][0]
except IndexError :
count = count[0]
#for fname in os.listdir( os.getcwd()+'/'+hobj.ddir+"/lattice/vdx/" ) :
# if ".txt" in fname :
# if "decomp" in fname and "_fs_" in fname :
# fspectdecomp = "{}/lattice/vdx/{}".format( hobj.ddir, fname )
# elif "_fs_" in fname :
# fspect = "{}/lattice/vdx/{}".format( hobj.ddir, fname )
# if ".dx" in fname :
# if "decomp" in fname and "_fs_" in fname :
# faxisdecomp = "{}/lattice/vdx/{}".format( hobj.ddir, fname )
# elif "_fs_" in fname :
# faxis = "{}/lattice/vdx/{}".format( hobj.ddir, fname )
nkgrid=[]
if args.decomp or args.decompall:
faxis = faxisdecomp
fspect = fspectdecomp
print ""
print "1:", faxis
print "2:", fspect
f = open(faxis, "r")
for line in f:
values = line.split()
if "KNAMES" in line:
knames = values[1:]
print knames
if "KC" in line:
kc = values[1]
if "KR" in line:
kr = values[1]
if "KPOINTS" in line:
nkgrid = values[1:]
nkgrid = np.array( nkgrid , dtype=int)