def macro(opts):
f = open(opts.outname + '.txt', 'r')
x = []
y = []
i = 1
for a in f:
if i == 1: i = i + 1
else:
x.append(float(a.split()[0]))
y.append(float(a.split()[1]))
l1 = opts.macro_len[
0] #4.2#abs(x_dipole[0] - x_dipole[1]) #length of 1st target phase
l2 = opts.macro_len[
1] # 4.0#unitcell[2][2] - l1 #length of 2nd target phase#
v_m_aver1, m_aver1 = jh.macroscopic_average(x, y, l1)
v_m_aver2, m_aver2 = jh.macroscopic_average(x, m_aver1, l2)
return x, m_aver2
def main(opts):
if check_the_input_path(opts.outname+'.txt'):
print("[CODE] There is output file ( %s )" %(opts.outname+'.txt'))
print("[CODE] Stop to re-reading/writing the potential")
print("[CODE] If you want to run, please remove the file or change the outputname (-o)")
elif check_the_input_path(opts.poscar) and check_the_input_path(opts.chg):
chg =read_CHGCHR_line(opts.chg)
length = len(chg)
unitcell, compound, position = jh.r_cryst_vasp(opts.poscar)
Volume = float(unitcell[0][0]) * float(unitcell[1][1]) * float(unitcell[2][2])
result=[]
f=open(opts.outname+'.txt','w' )
f.write(' %10.9s %30.20s %30.20s\n' \
%('height(A)', 'chg (e/A^3)', 'chg (e)'))
for a in range(length):
f.write(' %10.9s %30.20s %30.20s \n' \
%( float(unitcell[2][2])/length * a + float(unitcell[2][2])/length/2 , \
chg[a] / Volume , \
chg[a]))
else:
print('[ERROR] There is no input files')
print('[ERROR] Stop the calculation')
sys.exit()
####################################################################
if opts.plotting and check_the_input_path(opts.outname+'.txt'):
import matplotlib
import matplotlib.pyplot as plt
#set the figure format
width, height = opts.figsize
xmin, xmax = opts.xlim
dpi = opts.dpi
fig,(ax, ax0) = plt.subplots(2,1)
#if opts.macroscopic: fig,(ax, ax0) = plt.subplots(2,1)
#else: fig,(ax, ax0) = plt.subplots(2,1)
fig.set_size_inches(width, height)
fig.tight_layout(pad=0.50)
def set_plot(axx, opts):
if opts.plot_v == 2:
axx.set(xlabel='height(A)', ylabel=r'%s $(e)$' %opts.ylabel )
if opts.plot_v == 1:
axx.set(xlabel='height(A)', ylabel=r'%s $(e/A^3)$' %opts.ylabel )
if opts.grid: axx.grid()
axx.legend(fontsize='small',
frameon=True,
framealpha=0.6)
if opts.p_title:
str2 = os.getcwd().split('/') # get the title from the path
axx.set_title('%s of %s' % (str2[len(str2)-1], opts.p_title))
if xmax == 0: pass
else: axx.set_xlim([xmin,xmax])
if opts.plot_v == 2:
V = 1.
elif opts.plot_v == 1:
unitcell, compound, position = jh.r_cryst_vasp(opts.poscar)
V = float(unitcell[0][0]) * float(unitcell[1][1]) * float(unitcell[2][2])
with open(opts.outname + '.txt' , 'r') as f:
x=[]; y=[]; yp =[]; ym=[]; z=[]; i = 1 # ; NGZ = 0
y = []
y_a = []
y_b = []
for line in f:
if i == 1:
pass
else:
x.append(float(line.split()[0]))
y.append(float(line.split()[2])/V)
i = i + 1
ax.plot(x, y, '-', label=opts.label, color='black', linewidth=1)
####################################################################
if opts.macroscopic:
l1= opts.macro_len[0] #4.2#abs(x_dipole[0] - x_dipole[1]) #length of 1st target phase
l2= opts.macro_len[1]# 4.0#unitcell[2][2] - l1 #length of 2nd target phase#
print 'plotting macroscopic average (integrated twice with length scale of %s %s' %(l1, l2)
v_m_aver1, m_aver1 = jh.macroscopic_average(x,y,l1)
v_m_aver2, m_aver2 = jh.macroscopic_average(x,m_aver1,l2)
v_m_aver1, m_aver1 = jh.macroscopic_average(x,y,l1)
v_m_aver2, m_aver2 = jh.macroscopic_average(x,m_aver1,l2)
if opts.plotting:
ax0.plot(x, m_aver2, '-', label='2nd integration', color= 'red', linewidth=1)
####################################################################
if opts.plotting:
set_plot(ax,opts)#,opts.outname)
set_plot(ax0, opts)#,opts.outname+'0')
fig.tight_layout(pad=0.50)
fig.subplots_adjust(hspace= 0.30,\
left = 0.10,\
bottom= 0.10,\
right = 0.90,\
top = 0.90 \
)
plt.savefig(opts.outname+'.png', dpi=opts.dpi)
plt.show()
def main(opts):
if check_the_input_path(opts.outname + '.txt'):
print("[CODE] There is output file ( %s )" % (opts.outname + '.txt'))
print("[CODE] Stop to re-reading/writing the potential")
print(
"[CODE] If you want to run, please remove the file or change the outputname (-o)"
)
elif check_the_input_path(opts.poscar_AB) and check_the_input_path(opts.chg_ab) and \
check_the_input_path(opts.poscar_A) and check_the_input_path(opts.chg_a) and \
check_the_input_path(opts.poscar_B) and check_the_input_path(opts.chg_b):
chg_ab = read_CHGCHR_line(opts.chg_ab)
chg_a = read_CHGCHR_line(opts.chg_a)
chg_b = read_CHGCHR_line(opts.chg_b)
length = len(chg_ab)
unitcell, compound, position = jh.r_cryst_vasp(opts.poscar_AB)
Volume = float(unitcell[0][0]) * float(unitcell[1][1]) * float(
unitcell[2][2])
result = []
f = open(opts.outname + '.txt', 'w')
f.write(' %10.9s %30.20s %30.20s %30.20s %30.20s %30.20s \n' \
%('height(A)', 'cdd (e/A^3)', 'cdd (e)', 'chg_ab (e)','chg_a (e)', 'chg_b (e)'))
for a in range(length):
f.write(' %10.9s %30.20s %30.20s %30.20s %30.20s %30.20s \n' \
%( float(unitcell[2][2])/length * a + float(unitcell[2][2])/length/2 , \
(chg_ab[a] - chg_a[a] - chg_b[a]) / Volume , \
(chg_ab[a] - chg_a[a] - chg_b[a]), \
chg_ab[a], chg_a[a], chg_b[a]))
else:
print('[ERROR] There is no input files')
print('[ERROR] Stop the calculation')
sys.exit()
####################################################################
if opts.plotting and check_the_input_path(opts.outname + '.txt'):
import matplotlib
import matplotlib.pyplot as plt
#set the figure format
width, height = opts.figsize
xmin, xmax = opts.xlim
ymin, ymax = opts.ylim
dpi = opts.dpi
#fig,(ax, ax0) = plt.subplots(2,1)
if opts.macroscopic or opts.plot_all:
fig, (ax, ax0) = plt.subplots(2, 1)
else:
fig, (ax) = plt.subplots(1, 1)
fig.set_size_inches(width, height)
fig.tight_layout(pad=0.50)
option1 = {
'horizontalalignment': 'right',
'verticalalignment': 'baseline',
'fontsize': 10
} #, 'bbox':props}
option2 = {
'horizontalalignment': 'left',
'verticalalignment': 'baseline',
'fontsize': 10
} #, 'bbox':props}
def set_plot(axx, opts):
if opts.plot_v == 2:
axx.set(xlabel='height(A)', ylabel=r'%s $(e)$' % opts.ylabel)
if opts.plot_v == 1:
axx.set(xlabel='height(A)',
ylabel=r'%s $(e/A^3)$' % opts.ylabel)
if opts.grid: axx.grid()
axx.legend(fontsize='small', frameon=True, framealpha=0.6)
if opts.p_title:
str2 = os.getcwd().split('/') # get the title from the path
axx.set_title('%s of %s' % (str2[len(str2) - 1], opts.p_title))
if xmax == 0: pass
else: axx.set_xlim([xmin, xmax])
if ymax == 0: pass
else: axx.set_ylim([ymin, ymax])
if opts.plot_v == 2:
V = 1.
elif opts.plot_v == 1:
unitcell, compound, position = jh.r_cryst_vasp(opts.poscar_AB)
V = float(unitcell[0][0]) * float(unitcell[1][1]) * float(
unitcell[2][2])
with open(opts.outname + '.txt', 'r') as f:
x = []
y = []
yp = []
ym = []
z = []
i = 1 # ; NGZ = 0
y_ab = []
y_a = []
y_b = []
for line in f:
if i == 1:
pass
else:
x.append(float(line.split()[0]))
y.append(float(line.split()[2]) / V)
y_ab.append(float(line.split()[3]) / V)
y_a.append(float(line.split()[4]) / V)
y_b.append(float(line.split()[5]) / V)
if float(line.split()[2]) > 0:
yp.append(float(line.split()[2]) / V)
ym.append(0)
if float(line.split()[2]) < 0:
yp.append(0)
ym.append(float(line.split()[2]) / V)
i = i + 1
ax.plot(x, y, '-', label='Difference', color='black', linewidth=1)
if opts.plot_all:
ax0.plot(x, y_ab, '-', label='(AB)', color='black', linewidth=1)
ax0.plot(x, y_a, '--', label='(A)', color='silver', linewidth=1)
ax0.plot(x, y_b, '--', label='(B)', color='grey', linewidth=1)
ax.plot([], [],
linewidth=5,
label='Electron Accumulated',
color='r',
alpha=0.5)
ax.plot([], [],
linewidth=5,
label='Electron Loss',
color='g',
alpha=0.5)
ax.fill_between(x, yp, facecolor='r', alpha=0.5)
ax.fill_between(x, ym, facecolor='g', alpha=0.5)
####################################################################
if opts.cal_area or opts.macroscopic:
"""
Define the regions for area calculation (center of interface)
Condition for center of interface
1. Elements
2. Charge density (or potential density difference)
"""
x_dipole = []
centering = sum(x) / float(len(x))
unitcell, compound, position_b = jh.r_cryst_vasp(opts.poscar_B)
spcl = []
# 2nd phase coordinate list
#Get the max/min coordination for the defined 2nd phase
for a in position_b:
if a[opts.direction] > 0:
spcl.append(a[opts.direction])
else:
spcl.append(a[opts.direction] +
unitcell[opts.direction - 1][opts.direction -
1]) # Applying PBC
gap = max(x[len(x) - 1] - x[len(x) - 2],
spcl[len(spcl) - 1] - spcl[len(spcl) - 2]) * 2
# When the sign of charge/potential difference change,
pcc = [] # potential/charge density sign chage coordinate
for num in range(len(y) - 1):
if y[num] * y[num + 1] < 0.0: # and abs(x[num]- float(a)) < gap :
pcc.append(
x[num]) # potential/charge density sign chage coordinate
if len(pcc) > 2:
temp1 = []
temp2 = []
temp3 = []
less_cent = []
higher_cent = []
for a in pcc: # x_dipole:
if a < min(spcl):
temp1.append(a)
if a > max(spcl):
temp2.append(a)
x_dipole.append(max(temp1))
x_dipole.append(min(temp2))
elif (max(pcc) - centering) * (min(pcc) - centering) < 0:
x_dipole = pcc
if opts.cal_area:
if opts.plotting:
for a in set(x_dipole):
ax.plot([a, a], [min(y), max(y)],
'--',
color='black',
linewidth=1)
## Calculate Area
import numpy as np
from numpy import trapz
dist_r11 = []
dist_r12 = []
dist_r21 = []
dist_r22 = []
chg_q11 = []
chg_q12 = []
chg_q21 = []
chg_q22 = []
D_qor11 = []
D_qor12 = []
D_qor21 = []
D_qor22 = []
for num in range(len(y)):
if x[num] < min(x_dipole) or x[num] == min(x_dipole):
dist_r11.append(x[num])
chg_q11.append(y[num])
D_qor11.append(y[num] / x[num])
elif x[num] > min(x_dipole) and x[num] < centering:
dist_r12.append(x[num])
chg_q12.append(y[num])
D_qor12.append(y[num] / x[num])
elif x[num] < max(x_dipole) and x[num] > centering or x[
num] == max(x_dipole):
dist_r21.append(x[num])
chg_q21.append(y[num])
D_qor21.append(y[num] / x[num])
else:
dist_r22.append(x[num])
chg_q22.append(y[num])
D_qor22.append(y[num] / x[num])
print("area1-1 = %.12f; Dipole1-1 = %.12f" %
(trapz(chg_q11, dist_r11), sum(D_qor11)))
print("area1-2 = %.12f; Dipole1-2 = %.12f" %
(trapz(chg_q12, dist_r12), sum(D_qor12)))
print("area2-1 = %.12f; Dipole2-1 = %.12f" %
(trapz(chg_q21, dist_r21), sum(D_qor21)))
print("area2-2 = %.12f; Dipole2-2 = %.12f" %
(trapz(chg_q22, dist_r22), sum(D_qor22)))
if opts.plotting:
# props = dict(boxstyle='round', facecolor='wheat', alpha=0.5)
ax.text(x_dipole[0] * 0.99,
max(y) * 0.95,
r'%.5f (1-1)$\rightarrow$' % (trapz(chg_q11, dist_r11)),
**option1)
ax.text(x_dipole[0] * 1.01,
max(y) * 0.90,
r'$\leftarrow$(1-2) %.5f' % (trapz(chg_q12, dist_r12)),
**option2)
ax.text(x_dipole[1] * 0.99,
max(y) * 0.95,
r'%.5f (2-1)$\rightarrow$' % (trapz(chg_q21, dist_r21)),
**option1)
ax.text(x_dipole[1] * 1.01,
max(y) * 0.90,
r'$\leftarrow$(2-2) %.5f' % (trapz(chg_q22, dist_r22)),
**option2)
####################################################################
if opts.macroscopic:
print opts.macro_len
l1 = opts.macro_len[
0] #4.2#abs(x_dipole[0] - x_dipole[1]) #length of 1st target phase
l2 = opts.macro_len[
1] # 4.0#unitcell[2][2] - l1 #length of 2nd target phase#
v_m_aver1, m_aver1 = jh.macroscopic_average(x, y, l1)
v_m_aver2, m_aver2 = jh.macroscopic_average(x, m_aver1, l2)
v_m_aver1_ab, m_aver1_ab = jh.macroscopic_average(x, y_ab, l1)
v_m_aver2_ab, m_aver2_ab = jh.macroscopic_average(x, m_aver1_ab, l2)
sum_m1 = 0
i = 0
i2 = []
for a in range(len(x)):
if ( x[a] - min(x_dipole) ) * ( x[a] - max(x_dipole) ) < 0 and \
abs(x[a] - centering) < (max(x_dipole) -min(x_dipole) ) / 6:
sum_m1 = sum_m1 + m_aver2_ab[a]
i = i + 1
if max(m_aver2_ab) == m_aver2_ab[a]: i2 = a
sum_M1 = sum_m1 / i
if (m_aver2_ab[i2] - sum_M1) * (m_aver2_ab[0] - sum_M1) < 0:
sum_M2 = max(m_aver2_ab)
else:
sum_M2 = min(m_aver2_ab)
print "MACROSCOPIC AVERAGE: min - %s , max-of-center-regiron: %5.4f" \
%(min(m_aver2_ab), sum_m1/i)
print "MACROSCOPIC AVERAGE: diff: %5.4f" % (sum_m1 / i -
min(m_aver2_ab))
if opts.plotting:
if opts.plot_all:
ax0.plot(x,
m_aver1_ab,
'--',
label='1st integration',
color='blue',
linewidth=1)
ax0.plot(x,
m_aver2_ab,
'-',
label='$\Delta \widebar \\rho$',
color='red',
linewidth=1)
ax0.plot([min(x), centering], [sum_M1, sum_M1],
':',
color='red',
linewidth=1)
ax0.plot([min(x), centering], [sum_M2, sum_M2],
':',
color='red',
linewidth=1)
arwx0 = (min(x) + centering) / 6
arwy0 = min(sum_M2, sum_M1)
darwx = 0
darwy = abs(sum_M1 - sum_M2)
ax0.arrow(arwx0,
arwy0,
darwx,
darwy,
color='red',
head_width=min(.5, darwy / 10),
head_length=darwy / 6,
length_includes_head=True,
linewidth=1)
ax0.text(arwx0, arwy0 + darwy / 3, r'%.3f' % (darwy), **option2)
####################################################################
if opts.plotting:
set_plot(ax, opts) #,opts.outname)
if opts.macroscopic: set_plot(ax0, opts) #,opts.outname+'0')
fig.tight_layout(pad=0.50)
fig.subplots_adjust(hspace= 0.30,\
left = 0.20,\
bottom= 0.10,\
right = 0.90,\
top = 0.90 \
)
plt.savefig(opts.outname + '.png', dpi=opts.dpi)
plt.show()
