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draw_tl2_transition_levels.py
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# In[1]:
import numpy as np
import matplotlib.pyplot as plt
from matplotlib.ticker import MultipleLocator
import os
import sys
sys.path.append(os.environ['SCRIPT'])
# this file plots the transition levels
# Go to a graphdata folder, run 'python ${SCRIPT}/draw_transition_levels.py *.txt'
# the last argument is the file with transition level data stored in ${ZEROFOL}/berylliumO/graphdata
# format1: use straight lines to represent VB, CB
# format2: use blue regions to represent VB, CB
SMALL_SIZE = 12
MEDIUM_SIZE = 14
BIGGER_SIZE = 16
plt.rc('font', size=BIGGER_SIZE) # controls default text sizes
plt.rc('axes', titlesize=BIGGER_SIZE) # fontsize of the axes title
plt.rc('axes', labelsize=MEDIUM_SIZE) # fontsize of the x and y labels
plt.rc('xtick', labelsize=SMALL_SIZE) # fontsize of the tick labels
plt.rc('ytick', labelsize=SMALL_SIZE) # fontsize of the tick labels
plt.rc('legend', fontsize=SMALL_SIZE) # legend fontsize
plt.rc('figure', titlesize=BIGGER_SIZE) # fontsize of the figure title
plt.figure(figsize=(6,5),dpi=200)
if len(sys.argv)>1:
filename=sys.argv[1]
else:
print('Error! input the file to draw as an argument')
sys.exit()
# Define the function to read transition levels
def read_transition_level(filename):
with open(filename, 'r') as f:
lines = f.readlines() # lines is a LIST, different line contents are separated with '\n' at the end
defecttypes=[] # list of defect types
charges={} # dictionary, keyword is defecttypes
fermilevels={} # dictionary, keyword is defecttypes
for i in range(len(lines)):
splitted1=lines[i].split('DEFECTTYPE=') # for one type of defect
if len(splitted1)>1: ## if contains keyword DEFECTTYPE
#keyword=splitted[0].split('#')[-1].split()[-1] # keyword in INCAR: the changes are '#MAGMOM'->'MAGMOM'
defecttypes.append(splitted1[1].split('#')[0].split('!')[0]) # values of defect type like $\mathrm{Be}_\mathrm{O}$
splitted2=lines[i+1].split('TRANSITIONCHARGE=')[1] # n charges
splitted3=lines[i+2].split('TRANSITIONFERMILEVEL=')[1] # n-1 transition levels + 2 end points; end points (VBM, CBM) are same for all defects
charges[defecttypes[-1]]=np.array(splitted2.split()).astype(float)
fermilevels[defecttypes[-1]]=np.array(splitted3.split()).astype(float)
return defecttypes, charges, fermilevels
defecttypes, charges, fermilevels=read_transition_level(filename) # a dictionary
def charge_format(charge):
if charge == 0:
return '0'
elif charge == 1:
return '+'
elif charge == -1:
return '-'
elif charge > 0 :
return '%d+' % charge
else:
return '%d-' % abs(charge)
ax=plt.subplot(111)
num_defect = len(defecttypes) # split x axis in 2*num_defect segments -> Use 1/(2*num_defect) as the length of each piece
xlimits=[0,2*num_defect]
# two ends split one piece, so the segments are [0.5, 1.7], [2.5, 3.7], ...
ax.set_xlim(xlimits)
xx = np.array([0.5, 1.7]) # the length for the first one. Will iterate by xx=xx+2
xticks = range(1,2*num_defect,2)
write_transitionlevels=False
level_fontsize=12 # transition level font size
for defect_one in defecttypes:
print(defect_one)
defect_charge = charges[defect_one]
defect_fermilevel = fermilevels[defect_one]
maxy = defect_fermilevel[-1]
for i in range(1, len(defect_fermilevel)-1):
yy = defect_fermilevel[i]
yy = [yy, yy]
ax.plot(xx, yy, color='tab:red')
# write energy of transition levels above the level line
#plt.text(xx[0],yy[0]+maxy/200, '%s/%s %.2f'%(charge_format(defect_charge[i-1]), charge_format(defect_charge[i]),yy[0] ) )
tolerance = 0.6
if write_transitionlevels:
if defect_fermilevel[i+1]-yy[0]> tolerance:
plt.text(xx[0],yy[0]+maxy/200, '%s/%s %.2f'%( charge_format(defect_charge[i-1]), charge_format(defect_charge[i]),yy[0] ), fontsize=level_fontsize )
else:
plt.text(xx[0],yy[0]-maxy/25, '%s/%s %.2f'%(charge_format(defect_charge[i-1]), charge_format(defect_charge[i]),yy[0] ),fontsize=level_fontsize)
else:
if defect_fermilevel[i+1]-yy[0]> tolerance:
plt.text(xx[0],yy[0]+maxy/200, '%s/%s'%(charge_format(defect_charge[i-1]), charge_format(defect_charge[i]) ), fontsize=level_fontsize )
else:
plt.text(xx[0],yy[0]-maxy/24, '%s/%s'%(charge_format(defect_charge[i-1]), charge_format(defect_charge[i]) ),fontsize=level_fontsize )
# write the charge transitions below the level line
#plt.text(xx[0],yy[0]-maxy/40, )
xx = xx+2
bandgap=defect_fermilevel[-1]-defect_fermilevel[0]
xlabel=''
xlabelunit=''
ylabel='Energy'
ylabelunit='[eV]'
plt.ylabel(ylabel+ylabelunit) # y label
comment=(filename.split('rich_')[-1]).split('_transitionlevel')[0]
## set x tick labels to defect types
ax.set_xticks(xticks) # make sure the tick occupies the right position, with the right interval
ax.set_xticklabels(defecttypes, fontsize=BIGGER_SIZE) # changes the x tick labels
# draw VB CB blue regions
cbmregion = 2
vbmregion = 2
largestx=xlimits[1]
x=np.linspace(0,largestx,50)
ax.fill_between(x,-vbmregion, 0, color='skyblue') #defectenergyCBM,defectenergyCBM+cbmregion)
ax.fill_between(x,bandgap,bandgap+cbmregion,color='skyblue') #'#1f77b4') # defectenergyVBM,defectenergyVBM-vbmregion)
plt.text( largestx/15,-vbmregion+0.6,'VB' ) # text of valence band
plt.text( largestx/15, bandgap+vbmregion-1.4,'CB' ) # text of conduction band
ax.set_ylim([defect_fermilevel[0]-vbmregion,defect_fermilevel[-1]+cbmregion])
## spine: make y axis appear, x axis disappear
import matplotlib.ticker as tck
ax.spines['left'].set_linewidth(1.5) # set the length of spines
ax.spines['right'].set_linewidth(1.5)
ax.spines['top'].set_linewidth(1.5)
ax.spines['bottom'].set_linewidth(1.5)
## locator: x only need labels, no locator.
#ax.xaxis.set_major_locator(MultipleLocator(0.5)) # MultipleLocator the interval between y axis major ticks, like 0-0.5-1-1.5-...
#ax.yaxis.set_major_locator(MultipleLocator(5)) # MultipleLocator the interval between y axis major ticks, like 0-5-10
ax.yaxis.set_minor_locator(tck.AutoMinorLocator()) # have y minor ticks
#ax.xaxis.set_minor_locator(tck.AutoMinorLocator()) # don't want x ticks, don't uncomment this line
plt.tick_params(axis='y', which='minor', width=1., length=2, color='k', right=True)
plt.tick_params(axis='y', width=2,length=4) #, labelsize=15
#plt.tick_params(axis='x', length=0) # length=0 makes the major tick disappear, works the same as next line, which='minor', width=1.5,, color='k', right=True
# remove x major locators, add y major locators on the right.
ax.tick_params(top=False,bottom=False,right=True,left=True) # whether the major ticks will appear
plt.xticks(rotation=-35)
# save
figname= 'graph_%s_y%s_x%s.pdf' % (comment.replace(' ','_'), ylabel.replace(' ','_'), xlabel.replace(' ','_'))
print('\tremotesync \n%s' % (figname))
plt.tight_layout()
plt.savefig(figname, dpi=600)
plt.close()
#plt.show()