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band_orbit_dos.py
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band_orbit_dos.py
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#!/usr/local/Python-2.7.3/bin/python2.7
import matplotlib.pyplot as plt
import numpy as np
import sys, itertools
from matplotlib import rcParams, gridspec
from matplotlib import rc
import mpl_toolkits.axisartist as axisartist
from vaspData import readKPOINTS_linemode, readDOSCAR, readPROCAR, readCONTCAR, getVBM, getEgap
if __name__ == '__main__':
#rc('font',**{'family':'sans-serif','sans-serif':['Times New Roman']})
## for Palatino and other serif fonts use:
#rc('font',**{'family':'serif','serif':['Times New Roman']})
# use usetex=True for publish quality
# rc('text', usetex=False)
#rc('text', usetex=True)
params = {'backend': 'ps',
'text.latex.preamble': [r"\usepackage{upgreek}",
r"\usepackage{siunitx}",
r"\usepackage{amsmath}",
r"\usepackage{amstext}",],
'axes.labelsize': 16,
#'axes.linewidth': 1,
#'text.fontsize':17,
'legend.fontsize': 14,
'xtick.labelsize': 16,
# 'xtick.major.pad' : 6, # distance to major tick label in points
# 'xtick.minor.pad' : 6, # distance to the minor tick label in points
'ytick.major.pad' : 6, # distance to major tick label in points
'ytick.minor.pad' : 6, # distance to the minor tick label in points
#'xtick.major.width' : 0.75,
'ytick.labelsize': 16,
# 'figure.figsize': [8.8,6.8],
# 'text.usetex': True,
'axes.unicode_minus': True,
'ps.usedistiller' : 'xpdf'}
rcParams.update(params)
# rcParams.update({'figure.autolayout':True})
def readBand_KPOINTS(fileName ='EIGENVAL', NELECT = 0, kpoints_file = 'KPOINTS'):
# read EIGENVAL
f=open(fileName)
buffer=f.readlines()
f.close()
[nElect,nKpt,nBand]=[int(i) for i in buffer[5].split()][:]
#print [nElect, nBand,nKpt]
# VBM = getVBM(nElect/2, fileName)
bandInfo = []
kpoints =[]
eigenvals =np.zeros((nBand,nKpt))
for j in range(nKpt):
kpoint =np.array(buffer[-1 + 8 + (nBand+2)*j].split())[:3]
kpoint = np.array([float(k) for k in kpoint])
kpoints.append(kpoint)
for i in range(nBand):
eigenval = buffer[i + 8 + (nBand+2)*j].split()
eigenval = float(eigenval[1])
eigenvals[i,j] = eigenval
nkpt_line, specialKPName = readKPOINTS_linemode(fileName = kpoints_file)
specialKPPos = [i for i, k in enumerate(kpoints) if i == 0 or (i+1) % nkpt_line == 0]
#print specialKPName
VBM = eigenvals[nElect/2-1,:].max()
VBM = getVBM(fileName)
return kpoints,eigenvals - VBM , specialKPPos, specialKPName
def drawBand(eigenval='EIGENVAL', isLine=True, ax=''):
if ax=='':ax=plt
kpts, eigvals, specialKPPos, specialKPName = readBand_KPOINTS(eigenval)
# print specialKPPos, specialKPName
kpts.append(kpts[0])
x = [ np.linalg.norm(kpts[i] - kpts[i-1]) for i,k in enumerate(kpts)]
x = x[:-1]
x = [dist if dist<0.3 else 0 for dist in x]
x = np.cumsum(x)
for i in specialKPPos:
ax.axvline(x=x[i],color = 'k')
if isLine == True:
for band in eigvals:
ax.plot(x,band,'k-')
else:
X = np.tile(x,eigvals.shape[0],)
Y = eigvals.flatten()
plt.plot(X,Y,'ro', alpha = 0.3, )
ax.set_xticks(x[specialKPPos])
ax.set_xticklabels(specialKPName)
ax.set_xlim((x.min(),x.max()))
def orbitColor(proj, opt='spd'):
if opt == 'spd':
s = proj[0]
if len(proj)>4:
p = np.sum(proj[1:4])
d = np.sum(proj[4:9])
else :
p = proj[1]
d = proj[2]
c = np.array([s,p,d])/(np.max([s,p,d]))
return c
elif opt == 'dz2':
dz2 = proj[6]/np.sum(proj[:-1])
return (1-dz2,1,1)
def kpt_length(kpts):
latConst, latticeVecs, atomSetDirect = readCONTCAR(fileName='CONTCAR')
a, b, c = ([lat for lat in latticeVecs])
G_a = 2 * np.pi * np.cross(b, c) / np.dot(c, np.cross(a, b))
G_b = 2 * np.pi * np.cross(c, a) / np.dot(c, np.cross(a, b))
G_c = 2 * np.pi * np.cross(a, b) / np.dot(c, np.cross(a, b))
scale = np.array([np.linalg.norm(v) for v in [G_a, G_b, G_c]])
kpts = [kpt * scale for kpt in kpts]
kpts.append(kpts[0])
x = [ np.linalg.norm(kpts[i] - kpts[i-1]) for i,k in enumerate(kpts)]
x = x[:-1]
x = [dist if dist < 0.3 * np.min(scale) else 0 for dist in x]
x = np.cumsum(x)
return x
def draw_band_orbit(procar = 'PROCAR', eigenval = 'EIGENVAL', isLine = True, ax=''):
if ax=='':ax=plt
kpts, eigvals, specialKPPos, specialKPName = readBand_KPOINTS(eigenval)
# kpts.append(kpts[0])
# x = [ np.linalg.norm(kpts[i] - kpts[i-1]) for i,k in enumerate(kpts)]
# x = x[:-1]
# x = [dist if dist<0.3 else 0 for dist in x]
# x = np.cumsum(x)
x = kpt_length(kpts)
opt = 'spd'
PROCAR = readPROCAR(procar)
proj = PROCAR[5]
proj = np.sum(proj,axis=2)
proj = proj.reshape(np.prod(proj.shape)/proj.shape[-1],proj.shape[-1])
color = np.array([orbitColor(p, opt ) for p in proj])
Egap = getEgap(eigenval)
if Egap > 0:
ax.axhspan(0, Egap, lw = 0, facecolor = '0.5', alpha = 0.2)
for i in specialKPPos:
ax.axvline(x=x[i],color = 'k')
if isLine:
for band in eigvals:
ax.plot(x,band,'k-')
elif True:
# print color.shape
# print eigvals.shape
for i, band in enumerate(eigvals):
ax.plot(x,band,'o', c = color[i], markeredgewidth = 0, alpha = .5)
for i, band in enumerate(eigvals):
ax.plot(x,band,'o', c = color[i], markeredgewidth = 0, alpha = .5)
# for i, band in enumerate(eigvals[::-1]):
# ax.plot(x,band,'o', c = color[-i -1], markeredgewidth = 0, alpha = 1)
# for i, band in enumerate(eigvals[::-1]):
# ax.plot(x,band,'o', c = color[-i - 1], markeredgewidth = 0, alpha = 0.5)
else:
X = np.tile(x,eigvals.shape[0],)
Y = eigvals.flatten()
plt.plot(X,Y,'ro', alpha = 0.3, )
ax.set_xticks(x[specialKPPos])
ax.set_xticklabels(specialKPName)
ax.set_xlim((x.min(),x.max()))
def drawDOS(doscar="",atomNum=0,ax='',symbol='-',dos='tspd',legend=[],factor=1.):
if ax=='':ax=plt
#eSet,tDOSSet,sDOSSet,pDOSSet,dDOSSet = readPDOS(doscar,atomNum)
eSet,tDOSSet,sDOSSet,pDOSSet,dDOSSet = readDOSCAR(doscar,atomNum)
# plt.plot(eSet,sDOSSet)
# print eSet.shape, sDOSSet.shape
mozala = len(dos) - len(legend)
if mozala>0:
# legend += [''] *mozala
legend = [s for s in dos]
legend = legend[::-1]
if 't' in dos:
ax.plot(tDOSSet*factor,eSet,symbol,label=legend.pop())
if 's' in dos:
ax.plot(sDOSSet*factor,eSet,symbol,label=legend.pop()) #Si$_{}$
if 'p' in dos:
ax.plot(pDOSSet*factor,eSet,symbol,label=legend.pop()) #Si$_{}$
if 'd' in dos:
ax.plot(dDOSSet*factor,eSet,symbol,label=legend.pop()) #Si$_{}$
handles, labels = ax.get_legend_handles_labels()
max_dos = (np.average(tDOSSet) * 15 / 10.) * factor
ax.set_xlim((0, max_dos ))
leg=ax.legend(handles, labels, \
frameon=False ,loc='best',numpoints=1,handletextpad=0.5,borderpad=0.2, labelspacing=0.2, handlelength=1 )
# for t in leg.get_texts():
# t.set_fontsize(legendFontSize)
if __name__ == '__main__':
# if False:
''' ================================================ setting ================================================ '''
fig = plt.figure(figsize=(10,7))
plt.subplots_adjust(top=0.92,bottom=0.10, left =0.12 ,right =0.97, wspace=0.0,hspace=0.0)
gs = gridspec.GridSpec(2, 2,
width_ratios=[2,1],
height_ratios=[0.05,1])
eMin , eMax = -15, 10
EigenvalFile = "EIGENVAL"
DoscarFile = "DOSCAR"
''' ================================================ draw band ==================================== '''
ax_band = fig.add_subplot(axisartist.Subplot(fig,gs[:,:1]))
ax_band.set_ylim((eMin , eMax))
ax_band.set_ylabel('Energy (eV)')
# drawBand(EigenvalFile,ax=ax_band)
draw_band_orbit(procar = 'PROCAR', eigenval = EigenvalFile, isLine = False, ax = ax_band)
''' ================================================ draw dos ===================================='''
ax_dos = fig.add_subplot(gs[:,1:2])
ax_dos.tick_params(direction='in', labelleft='off',labelright='off', labelbottom = 'off' )
ax_dos.set_ylim((eMin , eMax))
ax_dos.set_title('DOS')
drawDOS(DoscarFile,0, dos = 'tspd', ax= ax_dos)
# fig.savefig('Estruct16.eps')
# fig.savefig('Estruct16.pdf')
# fig.savefig('Estruct130.png')
plt.show()