def choose_cell(inputs):
print "doping the given structure ", inputs[1]
filename = inputs[1]
target_ele = inputs[2:]
# num_ta_ele = int(inputs[3])
# change_ele = inputs[4]
output_name = filename + '_targets.vasp'
unitcell, compound, position = jh.r_cryst_vasp(filename)
print "Among the elements in the target file %s containing," % filename, compound[
0], ", you choose:", target_ele
#print epsilon, unitcell
new_position = []
temp_position = []
for a in range(len(position)):
for b in target_ele:
if position[a][0] == b:
temp_position = position[a]
temp_position[0] = b
new_position.append(temp_position)
# print temp_position[0]
# print temp_position,num_ta_ele,target_ele
# for a in new_position:
# for a in new_position: print a
if len(new_position[0]) == 7 and opts.Selec == False:
select = False
else:
select = opts.Selec
new_compound, new_position1 = jh.component_from_positions(new_position)
jh.w_poscar(position = new_position1,\
compound = new_compound, \
filename = output_name, \
unitcell = unitcell, \
Selective = select)
def expand_cell(filename,expantion,output_name, Selec):
print( "[CODE] expand the given structure ", filename)
print( """[CODE] output: %s with selective dynamics %s""" %(output_name,out))
unitcell, compound, position = jh.r_cryst_vasp(filename)
unitcell, compound, position = jh.pst_cell_expansion(unitcell, position, expantion )
jh.w_poscar(position = position, \
compound = compound, \
filename = output_name,\
unitcell = unitcell, \
Selective= Selec)
def add_atom_in_box(totatom, cellpar, Box, InsertAtomDF, OutputPath, unitcell):
exAtomPosition = [[0 for i in range(3)] for j in range(totatom)]
N_Atoms = InsertAtomDF['N_atom'].values.tolist()
AtomName = InsertAtomDF['element'].values.tolist()
AtomRadious = InsertAtomDF['radious'].values.tolist()
LabelN = 0
maxAtom = N_Atoms[LabelN]
tot_attempt = 0
NewPositions = []
for newatom in range(totatom):
exatom = -1
while exatom < newatom and tot_attempt < totatom * 100:
NewAtomPosition = [cellpar[i] * random.random() for i in range(3)]
tot_attempt = tot_attempt + 1
if tot_attempt > totatom * 100: # Exit Loop if it takes too long
print("[CODE] WARNING!!! The LOOP TAKE TOO LONG")
break
if point_in_box_vector(NewAtomPosition, Box) == True:
i = 0
x = exAtomPosition[i]
while distance(NewAtomPosition,
x) > min(AtomRadious) * 2.5 and i < totatom:
i = i + 1
if exAtomPosition[i] != [0, 0, 0]: x = exAtomPosition[i]
else: break
if distance(NewAtomPosition, x) > min(AtomRadious) * 2.5:
exatom = totatom
else:
pass
if distance(NewAtomPosition, x) < 3:
pass
# print(distance(NewAtomPosition,x))
if newatom < maxAtom: pass
elif newatom == maxAtom:
LabelN = LabelN + 1
maxAtom = N_Atoms[LabelN] + maxAtom
NewPositions.append([
AtomName[LabelN], NewAtomPosition[0], NewAtomPosition[1],
NewAtomPosition[2], 'T', 'T', 'T'
])
NewCompound = jh.component_from_positions(NewPositions)
jh.w_poscar(NewPositions,
compound=NewCompound,
filename=OutputPath,
unitcell=unitcell,
Selective=True)
return True
def doping_cell(opts):
print "[CODE] doping the given structure ", opts.poscar
outname = opts.poscar + '_new.vasp'
unitcell, compound, position = jh.r_cryst_vasp(opts.poscar)
new_position = []
if len(opts.select) > 0:
i = 1
print '[CODE] You choose a mode to doping only -An-Atom %s%i to %s'\
%(opts.select[0][0], int(opts.select[0][1]), opts.select[0][2])
for a in range(len(position)):
temp_position = []
if position[a][0] == opts.select[0][0]:
if i == int(opts.select[0][1]):
temp_position = position[a]
temp_position[0] = opts.select[0][2]
new_position.append(temp_position)
else:
new_position.append(position[a])
i = i + 1
else:
new_position.append(position[a])
elif opts.target_ele and opts.dopant_ele:
wmin, wmax = opts.window
print '[CODE] You choose a mode to doping Atoms (%s) in specific region from %f to %f along z-axis to %s'\
%(opts.target_ele, wmin, wmax, opts.dopant_ele)
for a in range(len(position)):
temp_position = []
if position[a][0] == opts.target_ele and position[a][
3] < wmax and position[a][3] > wmin:
temp_position = position[a]
temp_position[0] = opts.dopant_ele
new_position.append(temp_position)
else:
new_position.append(position[a])
else:
print '[CODE] YOU NEED TO CHECK help (-h) option'
new_compound, new_position1 = jh.component_from_positions(new_position)
jh.w_poscar(position = new_position1, \
compound = new_compound, \
filename = outname, \
unitcell = unitcell, \
Selective = False)
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 add_atom_in_box(totatom, Box, InsertAtomDF, OutputPath, unitcell):
exAtomPosition = []
minDistance = InsertAtomDF['radious'].sum() / InsertAtomDF.shape[0] * 2.5
for j in range(InsertAtomDF.shape[0]):
label = InsertAtomDF.element.iloc[j]
N_atom = InsertAtomDF.N_atom.iloc[j]
for natom in range(N_atom):
exAtomPosition.append([label, 0, 0, 0, 'T', 'T', 'T'])
exAtomPositionDF = pd.DataFrame(
exAtomPosition, columns=['label', 'x', 'y', 'z', 'rx', 'ry', 'rz'])
for newatom in range(InsertAtomDF.N_atom.sum()):
tot_attempt = 0
condition = True
while condition and tot_attempt < InsertAtomDF.N_atom.sum() * 1000:
NewAtomPosition0 = [random.random() for i in range(3)]
while min(
np.dot(NewAtomPosition0, unitcell)
) < minDistance / 2 and tot_attempt < InsertAtomDF.N_atom.sum(
) * 1000:
NewAtomPosition0 = [random.random() for i in range(3)]
NewAtomPosition = np.dot(NewAtomPosition0, unitcell)
tot_attempt = tot_attempt + 1
exAtomPositionDF['distance'] = (
(exAtomPositionDF['x'] - NewAtomPosition[0])**2 +
(exAtomPositionDF['y'] - NewAtomPosition[1])**2 +
(exAtomPositionDF['z'] - NewAtomPosition[2])**2)**0.5
condition = exAtomPositionDF['distance'].min() < minDistance
# print(newatom, NewAtomPosition, exAtomPositionDF['distance'].min() > minDistance, min(NewAtomPosition))
exAtomPositionDF['x'].iloc[newatom] = NewAtomPosition[0]
exAtomPositionDF['y'].iloc[newatom] = NewAtomPosition[1]
exAtomPositionDF['z'].iloc[newatom] = NewAtomPosition[2]
NewPositions = exAtomPositionDF.iloc[:, 0:7].values.tolist()
NewCompound = jh.component_from_positions(NewPositions)
jh.w_poscar(NewPositions,
compound=NewCompound,
filename=OutputPath,
unitcell=unitcell,
Selective=True)
return True
def temp(filename):
i = 1
dist = 2
overlap = 6.87639 / 6 * 1
y_shift = 0.5
unitcell, compound, position = jh.r_cryst_vasp(filename)
spli = []
fermi = []
with os.popen("grep fermi OUTCAR |tail -1 | awk '{print $3}'") as a:
temp = 1
for line in a:
if temp == 1:
fermi = line
temp = +1
else:
pass
print "python /team/ptcad/jhlee/b_codework/py_vasp_post_process/py_vasp.dos.py \\"
print "-y 0 %10.3f -z %8.5s --notot -q -s 8 %i --fill -x -10 5 \\" \
%((unitcell[2][2] * y_shift +2)/dist , fermi, int(unitcell[2][2] / 2 / dist))
for a in range(int(unitcell[2][2] / dist) + 1):
temp = []
i = 1
speci = []
for x in position:
if x[3] > a * dist - overlap and x[3] < (a + 1) * dist + overlap:
temp.append(i)
speci.append(x[0])
i += 1
speci.sort(reverse=True)
# print "\
#python /team/ptcad/jhlee/b_codework/py_vasp_post_process/py_vasp.dos.py \
#-y 0 1.0 -z %8.5s --notot -q -s 8 2 --fill -x -10 5 --pdosoffset=%s\
#-p " %(fermi, str(a*dist)),
print "\\\n -p ",
for xx in temp:
print xx,
#print " --lc=%s --fill --fac=2 --pdosoffset=%f -l " %(color, y_shift),
print " --fill --fac=2 --pdosoffset=%f -l " % (y_shift),
for yy in set(speci):
sys.stdout.write(yy)
if 'Hf' in speci: color = 'black'
if 'Ti' in speci: color = 'blue'
print " --lc=%s " % (color),
def get_born_effective(opts):
in_unitcell, in_compound, in_position = jh.r_cryst_vasp(opts.poscar)
n_atom = len(in_position)
d = pd.DataFrame(
np.zeros((10, n_atom)),
columns=['atom', 'xx', 'xy', 'xz', 'yx', 'yy', 'yz', 'zx', 'zy', 'zz'])
j = 0
for a, b in zip(in_compound[0], in_compound[1]):
for i in range(int(b)):
d.atom.iloc[j] = a + '%s' % (int(i) + 1)
j = j + 1
if os.path.isfile(opts.outcar) == True:
strings = "BORN EFFECTIVE CHARGES (in e, cummulative output)"
start_num = read_file_line(opts.outcar, strings)
if start_num == 0: return d
else:
with open(opts.outcar, 'r') as f:
i = 0
for line in f:
if i > start_num + 1 and i < start_num + n_atom * 4 + 2:
if 'ion' in line:
index_num = int(line.split()[1]) - 1
if (i - start_num - 2) % 4 == 1:
for col_num in range(3):
d.iloc[index_num, col_num + 1] = float(
line.split()[col_num + 1])
elif (i - start_num - 3) % 4 == 1:
for col_num in range(3):
d.iloc[index_num, col_num + 4] = float(
line.split()[col_num + 1])
elif (i - start_num - 4) % 4 == 1:
for col_num in range(3):
d.iloc[index_num, col_num + 7] = float(
line.split()[col_num + 1])
i = i + 1
else:
print("[CODE] Error, There is no %s/OUTCAR" % filename)
return d
def main(opts):
#print "[CODE] Start to read the given structure: ", opts.poscar
unitcell, compound, position = jh.r_cryst_vasp(opts.poscar)
a = np.array(unitcell[0])
b = np.array(unitcell[1])
c = np.array(unitcell[2])
volume = np.dot(np.cross(a,b),c)
vec_a= np.sum(a**2) ** (0.5)
vec_b= np.sum(b**2) ** (0.5)
vec_c= np.sum(c**2) ** (0.5)
alpha= np.degrees(np.arccos(np.dot(b,c)/vec_b/vec_c))
beta = np.degrees(np.arccos(np.dot(a,c)/vec_a/vec_c))
gamma= np.degrees(np.arccos(np.dot(a,b)/vec_a/vec_b))
print('a %8.8s : %20.10f' %('alpha' ,alpha))
print('a %8.8s : %20.10f' %('beta' ,beta))
print('a %8.8s : %20.10f' %('gamma' ,gamma))
print('l %8.8s : %20.10f' %('vec_a' ,vec_a))
print('l %8.8s : %20.10f' %('vec_b' ,vec_b))
print('l %8.8s : %20.10f' %('vec_c' ,vec_c))
print('V %8.8s : %20.10f' %('volume',volume))
for a,b in zip(compound[0],compound[1]):
print('C %8.8s : %20.i' %(a,int(b)))
def main(opts):
print("[CODE] Start to read the given structure: ", opts.poscar)
if opts.out: output_name = opts.out
else: output_name = opts.poscar + '_targets.vasp'
new_position = []
temp_position = []
select = True
unitcell, compound, position = jh.r_cryst_vasp(opts.poscar)
if opts.condi:
print('[CODE] the -c option is chosen (not the elements)')
if opts.condi[1] < opts.condi[0]:
reverse = True
print('[CODE] [0] %f is higher than [1] %f' %
(opts.condi[0], opts.condi[1]))
print(
'[CODE] atoms higher than [0] %f and lower then [1] %f are chosen'
% (opts.condi[0], opts.condi[1]))
else:
reverse = False
print('[CODE] [1] %f is higher than [0] %f' %
(opts.condi[1], opts.condi[0]))
print('[CODE] choose element higher than %f and lower than %f' %
(opts.condi[0], opts.condi[1]))
for a in range(len(position)):
if opts.condi[0] > 1 or opts.condi[1] > 1: z = 1
else: z = unitcell[2][2]
if reverse:
if position[a][3]/z > opts.condi[0] or \
position[a][3]/z < opts.condi[1]:
# print a, len(new_position), position[a]
temp_position = position[a]
new_position.append(temp_position)
else:
if position[a][3]/z > opts.condi[0] and \
position[a][3]/z < opts.condi[1]:
# print position[a][3]/unitcell[2][2], opts.condi
temp_position = position[a]
new_position.append(temp_position)
else:
print(
"[CODE] Among the elements in the target file %s containing," %
opts.poscar, compound[0], ", you choose:", opts.t_ele)
for a in range(len(position)):
for b in opts.t_ele:
if position[a][0] == b:
temp_position = position[a]
temp_position[0] = b
new_position.append(temp_position)
if len(position[0]) == 7 and opts.selec == False:
select = False
else:
select = opts.selec
new_compound, new_position1 = jh.component_from_positions(new_position)
if len(new_position) == 0:
print("error!!!")
else:
jh.w_poscar(position = new_position1,\
compound = new_compound, \
filename = output_name, \
unitcell = unitcell, \
Selective = select)
#Purpose: Moving a poscar
import JH_lib as jh
import os
import numpy as np
from optparse import OptionParser
#1. Read.
import sys
if __name__ == '__main__':
from time import time
# filename = 'CONTCAR'
t0 = time()
filename = sys.argv[1]
## Lines for JH in SK hynix (180326)
unitcell, compound, position = jh.r_cryst_vasp(filename)
aver = 0
i = 0
for a in position:
aver += a[3]
i += 1
# print aver/float(i)
new_position = jh.pst_poscar_move(position, 0.0, 0.0, aver / float(i))
# if len(new_position[0]) == 7:
select = True
# else:
# select = False
jh.w_poscar(position,
compound=compound,
#!/bin/python
#Using code JH_lib
#Purpose: Moving a poscar
import JH_lib as jh
import os
#1. Read.
import sys
## Lines for JH in SK hynix (180326)
filename = sys.argv[1]
unitcell, compound, position = jh.r_cryst_vasp(filename)
print """
[CODE] run this commend with target POSCAR file name and expanded cell which you want:
[CODE] for example: python /team/ptcad/jhlee/b_codework/py_edit_poscar/change_unitcell.py POSCAR 0 0 15
[CODE] means: change cell with giving 0, 0, and 15 angstrom in x-axis and y-axis and keeping z-axis
[CODE] for the direction, please check after test this code.
[CODE] output: %s
""" % (filename + '_new.vasp')
new_unitcell = []
new_unitcell.append([
float(unitcell[0][0]) + float(sys.argv[2]), unitcell[0][1], unitcell[0][2]
])
new_unitcell.append([
unitcell[1][0],
float(unitcell[1][1]) + float(sys.argv[3]), unitcell[1][2]
])
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()
help='Turn on the Selective Dynamics to T T T(Default: False)')
return par.parse_args()
############################################################
if __name__ == '__main__':
from time import time
opts, args = command_line_arg()
t0 = time()
filename1 = opts.file1
filename2 = opts.file2
output_name = opts.out
## Lines for JH in SK hynix (180326)
unitcell1, compound1, position1 = jh.r_cryst_vasp(filename1)
unitcell2, compound2, position2 = jh.r_cryst_vasp(filename2)
if unitcell1 == unitcell2:
#pass
print "same!"
else:
print sys.stderr
new_position = position1 + position2
if len(new_position[0]) == 7 and opts.Selec == False:
select = False
else:
select = opts.Selec
new_compound, new_position1 = jh.component_from_positions(new_position)
jh.w_poscar(position = new_position1,\
############################################################
def check_potcar(elements):
f = open(opts.potcar_list, 'r')
for line in f:
if "'%s'" % elements in line:
return line.split()[2:]
if __name__ == '__main__':
opts, args = command_line_arg()
if opts.printout:
from time import time
t0 = time()
unitcell, compound, position = jh.r_cryst_vasp(opts.structure)
# print(compound[0],position)
x = jh.w_poscar(position,
filename=opts.structure + '.vasp',
unitcell=unitcell)
unitcell, compound, position = jh.r_cryst_vasp(opts.structure + '.vasp')
os.system('mv %s %s/POSCAR' % (opts.structure + '.vasp', opts.folderpath))
if opts.printout: print(compound[0], position)
commends = 'cat '
MetaList = []
for ele in compound[0]:
[PotcarName, Enmax, Valency, AtomicMass] = check_potcar(ele)
MetaDict = {
'element': ele,
'PotcarName': PotcarName,
return par.parse_args( )
####################################################################
####################################################################
if __name__ == '__main__':
from time import time
opts, args = command_line_arg()
t0 = time()
# filename1 = sys.argv[1]
# filename2 = sys.argv[2]
## Lines for JH in SK hynix (180326)
sub_unitcell, sub_compound, sub_position = jh.r_cryst_vasp(opts.filename1)
add_unitcell, add_compound, add_position = jh.r_cryst_vasp(opts.filename2)
z=[];
for a in sub_position:
z.append(a[3])
if opts.twoside:
min_add=[] ; max_add=[]
else: max_add=[]
for a in add_position:
if opts.twoside:
mi = - float(a[3]) + ( min(z) - opts.dist )
ma = float(a[3]) + ( max(z) + opts.dist )
min_add.append([a[0],a[1],a[2], mi])
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()
def plot_heatmat_dos(folderpath, ax, points=200, len_dos=1.5):
import JH_lib as jh
import pandas as pd
tdos, atoms = read_doscar(folderpath)
unitcell, compound, position = jh.r_cryst_vasp(folderpath + '/POSCAR')
surf = 0
for a in position:
if a[3] < 20 and a[3] > surf: surf = a[3]
plotting = False
plotting2 = False
plotting3 = True
ndos = len(tdos)
z_limits = [0, 20]
energy_limits = [-5, 5]
zlist = [z_limits[1] / points * i for i in range(points)]
df_plt = pd.DataFrame()
noverlap = np.zeros((int(ndos)))
for x in zlist:
df_plt['%2.1f' % x] = np.zeros((int(ndos)))
df = pd.DataFrame(tdos, columns=['level', 'tdos'])
ymax = ndos - int((df.level.max() - energy_limits[1]) /
((df.level.max() - df.level.min()) / ndos))
ymin = int((energy_limits[0] - df.level.min()) /
((df.level.max() - df.level.min()) / ndos))
print(ymax, ymin, surf)
ele = 1
for a in atoms:
df1 = pd.DataFrame(
a, columns=['atom%i_s' % ele,
'atom%i_p' % ele,
'atom%i_d' % ele])
df1['atom%i' %
ele] = df1['atom%i_s' % ele] + df1['atom%i_p' %
ele] + df1['atom%i_d' % ele]
df = pd.concat([df, df1], axis=1)
# print(df1['atom%i'%ele].min(), df1['atom%i'%ele].max())
if plotting:
zlevel = [position[ele - 1][3] for x in range(int(ndos))]
clevel = df1['atom%i' % ele]
plt.scatter(x=zlevel,
y=df.level,
s=0.1,
c=clevel,
cmap=plt.cm.rainbow)
plt.clim(10, 30)
if plotting2:
for zz in zlist:
if abs(position[ele - 1][3] - zz) < 1.0:
zlevel = [zz for i in range(int(ndos))]
clevel = df1['atom%i' % ele]
plt.scatter(x=zlevel,
y=df.level,
s=0.1,
c=clevel,
cmap=plt.cm.rainbow)
plt.clim(10, 15)
if plotting3:
for i in range(points):
zz = zlist[i]
if abs(position[ele - 1][3] - zlist[i]) < len_dos:
weight_dist = 1 - abs(position[ele - 1][3] -
zlist[i]) / len_dos
if df_plt['%2.1f' % zz].sum == 0:
# print('zero!')
df_plt['%2.1f' %
zz] = df1['atom%i' % ele] * weight_dist
else:
noverlap[i] = noverlap[i] + 1
df_plt['%2.1f' %
zz] = df1['atom%i' %
ele] * weight_dist + df_plt['%2.1f' %
zz]
ele = ele + 1
if plotting3:
import seaborn as sns
df_plt.index = df.level
if '01_GaN_0001_' in folderpath:
sns.heatmap(df_plt, vmin=0.10, vmax=1.5 / 4, ax=ax, cbar=False)
else:
sns.heatmap(df_plt, vmin=0.10, vmax=1.5, ax=ax, cbar=False)
ax.set(
ylim=[ymin, ymax],
xlabel='Distance $(\\rm \\AA)$',
ylabel='Energy Level (eV)',
yticks=[-5, 0, 5],
# xticks=[0,20],
)
filename = sys.argv[1]
epsilon = [float(sys.argv[2]), float(sys.argv[3]), float(sys.argv[4]) ]
print """
[CODE] run this commend with target POSCAR file name and strain which you want:
[CODE] for example: python /team/ptcad/jhlee/b_codework/py_edit_poscar/expand_poscar.py POSCAR 0.1 0.1 0
[CODE] means: expand cell with given strain 0.1 and 0.1 in x-axis and y-axis and keeping z-axis
[CODE] for some unit cell not keeping cubic/tetragonal like system (non-vertical), check the result
[CODE] output: %s
""" %(filename+'_new.vasp')
## Lines for JH in SK hynix (180326)
unitcell, compound, position = jh.r_cryst_vasp(filename)
#print epsilon, unitcell
for a in range(3):
for b in range(3):
# print a,b
unitcell[a][b] = float(unitcell[a][b]) * (1 + epsilon[a])
for a in range(len(position)):
position[a][1] = float(position[a][1]) * (1 + epsilon[0])
position[a][2] = float(position[a][2]) * (1 + epsilon[1])
position[a][3] = float(position[a][3]) * (1 + epsilon[2])
jh.w_poscar(position = position, \
compound = compound, \
filename = filename+'_new.vasp', \
############################################################
__version__ = "1.0"
############################################################
print """[CODE] run this commend with target POSCAR file name and distance which you want:
[CODE] for example: python /team/ptcad/jhlee/b_codework/py_move-poscar/move_poscar.py POSCAR 1 1 1
[CODE] means: moving atoms in given POSCAR 1 Angstrom in x-axis and 1 A in y-axis and 1 A z-axis
[CODE] for the direction, please check after test this code.
"""
if __name__ == '__main__':
from time import time
t0 = time()
filename = sys.argv[1]
unitcell, compound, position = jh.r_cryst_vasp(filename)
new_position = jh.pst_poscar_move(position, float(sys.argv[2]), \
float(sys.argv[3]),float(sys.argv[4]))
if len(new_position[0]) == 7:
select = True
else:
select = False
jh.w_poscar(position,
compound=compound,
filename='new.vasp',
unitcell=unitcell,
Selective=select)
t1 = time()
def main(opts):
print '''\
[CODE] Chosen input file:'''
if check_the_input_path(opts.poscar) and check_the_input_path(
opts.inputname):
pass
else:
print('[ERROR] Stop the calculation')
sys.exit
if check_the_input_path(opts.outname + '.txt'):
print('[CODE] there is same name for output, %s' % opts.outname)
print('[CODE] Skip the reading input file: %s' % opts.inputname)
#print('[ERROR] Stop the calculation')
else:
print('[CODE] Start to read input file: %s' % opts.inputname)
unitcell, compound, position = jh.r_cryst_vasp(opts.poscar)
total = read_potential_line(opts)
write_potential_line( unitcell =unitcell ,\
local_potental =total ,\
# plot =opts.plotting ,\
output_name =opts.outname ) # ,\
# ax =axx)
#sys.exit()
if opts.plotting:
print(
'''[CODE] Drawing: ON with output (-o, --outname) : %s .txt''' %
opts.outname)
#set the figure format
width, height = opts.figsize
xmin, xmax = opts.xlim
ymin, ymax = opts.ylim
if opts.macroscopic:
if opts.permit:
fig, (ax0, ax1, ax2) = plt.subplots(3, 1)
axx = ax0
else:
fig, (ax0, ax1) = plt.subplots(2, 1)
axx = ax0
else:
fig, ax0 = plt.subplots(1, 1)
axx = ax0
plot_1D_plot(opts.outname + '.txt', ax=ax0)
else:
axx = ''
print(
'''[CODE] Drawing: OFF (If you want: use -f with/without -o or --outname)'''
)
if opts.yyy:
f = open(opts.outname + '.txt', 'r')
x = []
y = []
i = 1
evac = 9999
for a in f:
if i == 1:
i = i + 1
ll = a.split()[1]
ef = float(a.split()[2])
else:
x.append(float(a.split()[0]))
y.append(float(a.split()[1]))
if float(a.split()[0]) > opts.yyy and evac == 9999:
evac = a.split()[1]
print(
"""
filename = %s
vaccume energy = %s
fermi energy = %s
work-function = %f
""" % (opts.outname + '.txt', evac, ef, float(evac) - float(ef)))
#Ef = read_fermi(opts)
if opts.macroscopic:
print(
'''[CODE] Calculating Macrocsropic average (differenticate) : ON '''
)
target = opts.outname + '.txt'
x, bar_V = macro(opts)
d_bar_V = np.zeros(bar_V.shape, np.float)
d_bar_V[0:-1] = np.diff(bar_V) / np.diff(x)
d_bar_V[-1] = (bar_V[-1] - bar_V[-2]) / (x[-1] - x[-2])
write_lines( x = x ,\
xh = 'dist' ,\
ys = [bar_V, d_bar_V] ,\
ysh = ['b', 'db'] ,\
output_name = opts.outname+'_m' )
if opts.permit:
p, pz = relative_permitivity(d_bar_V, x, opts.permit)
if opts.plotting:
if opts.macroscopic:
ax0.plot(x,
bar_V,
'-',
label=opts.label + '_macro',
color='red',
linewidth=1)
ax1.plot(x,
d_bar_V,
'-',
label=opts.label + '_macro_differ',
color='red',
linewidth=1)
if opts.permit:
ax2.plot(pz,
p,
'-',
label=opts.label,
color='red',
linewidth=1)
ax2.set_xlabel('relative permittivity $(1/\varepsilon)$')
if xmin == xmax: pass
else: ax0.set_xlim([xmin, xmax])
if ymin == ymax: pass
else: ax0.set_ylim([ymin, ymax])
fig.set_size_inches(width, height)
# ax0.yaxis.set_ticks(np.arange(ymin, ymax, 4))
# ax0.axes.get_yaxis().set_visible(True)
# plt.gca().set_aspect('equal', adjustable='box')
# fig.tight_layout(pad=0.50)
# ax0.legend(fontsize='small',
# frameon=True,
# framealpha=0.6)
# fig.subplots_adjust(left = 0.10,\
# bottom= 0.10,\
# right = 0.90,\
# top = 0.90 \
# )
plt.grid()
# plt.savefig(opts.outname+'.png', dpi=opts.dpi)
plt.show()
print('[CODE] Finish converting and writting')
def read_doscar_long(folderpath):
import JH_lib as jh
doscar = open(folderpath+'/DOSCAR', 'r')
start_atom_dos=False
len_pdos, maxdos, mindos, ndos, efermi,temp , natom= 0,0,0,0,0,0,0
i = 1 ; atoms=[]
for line in doscar:
# try:
if i == 6:
[maxdos, mindos, ndos, efermi,temp] = line.split()
column=['level','tdos']
tdos=np.zeros((int(ndos),2))
elif i > 6 and i < 6 + (1 + int(ndos)) * 1:
tdos[i-7] = [float(xx)-float(efermi) for xx in line.split()[:2]]
elif i == 7 + int(ndos):
natom=1
elif i > 6 + (1 + int(ndos)) * natom and i < 6 + (1 + int(ndos)) * (natom+1):
if start_atom_dos:
# print(line, i- 7 - (1 + int(ndos)) * (natom), atom_dos.shape)
atom_dos[i- 7 - (1 + int(ndos)) * (natom)] = [float(xx) for xx in line.split()[1:]]
else:
start_atom_dos = True
len_pdos = len(line.split()[1:])
atom_dos=np.zeros(((int(ndos),len_pdos)))
# print(line, i- 7 - (1 + int(ndos)) * (natom), atom_dos.shape)
elif i == 6 + (1 + int(ndos)) * (natom+1) :
if natom != 0:
atoms.append(atom_dos)
atom_dos=np.zeros(((int(ndos),len_pdos)))
natom = natom + 1
i = i + 1
unitcell, compound, position = jh.r_cryst_vasp(folderpath+'/POSCAR')
df_plt= pd.DataFrame()
df = pd.DataFrame(tdos, columns=['level','tdos'])
i=1 ; num = 1; element=''
for a in atoms:
if position[i-1][0] == element: ele = '%s%i' %(element,i)
else:
num = 1
ele = '%s%i' %(position[i-1][0],num)
element = position[i-1][0]
if len_pdos == 9:
colname=['%s_s'%ele,'%s_px'%ele, '%s_py'%ele,'%s_pz'%ele,
'%s_dxy'%ele,'%s_dyz'%ele,'%s_dz2r2'%ele,'%s_dxz'%ele,'%s_dx2y2'%ele]
df1 = pd.DataFrame(a, columns=[colname])
df1['%s_p'%ele] = df1[colname[1:4]].sum(axis=1)
df1['%s_d'%ele] = df1[colname[4:]].sum(axis=1)
df1['%s'%ele] = df1[colname].sum(axis=1)
elif len_pdos == 3:
colname=['%s_s'%ele,'%s_p'%ele, '%s_d'%ele]
df1 = pd.DataFrame(a, columns=[colname])
df1['%s'%ele] = df1[colname].sum(axis=1)
df = pd.concat([df, df1], axis=1)
i = i+1 ; num = num + 1
new_colname =['level', 'tdos']
for x in df.columns[2:]:
new_colname.append(x[0])
df.columns = new_colname
return df, position
def main(opts):
print("[CODE] Start to read the given structure: ", opts.poscar)
# Read a POSCAR and write to a CIF.
path1 = opts.path
path2 = path1 + '/xx_SOD_FINDSYM'
path3 = path2 + '/0_pre_SOD_FINDSYM'
path4 = path2 + '/1_SOD'
os.system('mkdir %s' % path2)
os.system('mkdir %s' % path3)
os.system('mkdir %s' % path4)
print("[CODE] Generate the program output in %s", path2)
repeat = opts.expand
print("[CODE] Doping with expanding structure:", repeat)
unitcell, compound, position = jh.r_cryst_vasp('%s' % opts.poscar)
structure = pmg.Structure.from_file(opts.poscar)
structure.to(filename=path3 + "/POSCAR.cif")
# findsym running
commends ='cd ' + path3 + '; bash '+ opts.findsym +'/findsym.sh %s %s %s' \
%("./POSCAR.cif", './POSCAR.in', "./POSCAR.iso")
os.system(commends)
target = []
i = 0
start = False
f = open(path3 + "/POSCAR.iso", 'r')
for line in f:
if start:
# print(line)
if len(line.split()) > 1:
target.append(line.split()[1].split(','))
if 'Space Group' in line:
head = line
if '_space_group_symop_operation_xyz' in line:
start = True
if start:
if 'loop_' in line:
start = False
# print(targlet)
print_out = False
f2 = open(path4 + "/SGO", 'w')
f2.write('%s' % head)
if print_out: print('%s' % head, end='')
for temp in range(len(target)):
output_m = []
output_shift = []
for temp1 in range(3):
if len(target[temp][temp1].split('+')) == 1:
output_m.append(
from_operation_xyz_to_matrix(target[temp][temp1]))
output_shift.append('0')
if len(target[temp][temp1].split('+')) == 2:
output_m.append(
from_operation_xyz_to_matrix(
target[temp][temp1].split('+')[0]))
output_shift.append(target[temp][temp1].split('+')[1])
f2.write('%1.0i\n' % (temp + 1))
if print_out: print('%1.0i' % (temp + 1))
# output_m = [[1, 0, 0], [2, 1, 0], [3, 0, 1]]
for temp1 in range(3):
for temp2 in range(3):
f2.write("%4.1i" % output_m[temp1][temp2]) #,end='')
if print_out: print("%4.1i" % output_m[temp1][temp2], end='')
f2.write("%6.1f\n" %
(from_operation_shift_to_matrix(output_shift[temp1])))
if print_out:
print("%6.1f" %
(from_operation_shift_to_matrix(output_shift[temp1])))
f2.write('0\n')
if print_out: print(0)
f2.close()
commends = 'python2 %s/poscar_info.py -p %s > %s/out.txt' % (
opts.python_jh, opts.poscar, path3)
os.system(commends)
element = []
Nelement = []
with open('%s/out.txt' % path3, 'r') as f:
for line in f:
if 'C ' in line:
element.append(line.split()[1])
Nelement.append(line.split()[3])
elif 'l ' in line:
if 'vec_a' in line: len_a = float(line.split()[3])
elif 'vec_b' in line: len_b = float(line.split()[3])
elif 'vec_c' in line: len_c = float(line.split()[3])
elif 'a ' in line:
if 'alpha' in line: alpha = float(line.split()[3])
elif 'beta' in line: beta = float(line.split()[3])
elif 'gamma' in line: gamma = float(line.split()[3])
elif 'V ' in line:
if 'vo' in line: volume = line.split()[3]
os.system('rm %s/out.txt' % path3)
# print(element)
f3 = open('%s/INSOD' % path4, 'w')
f3.write('''#Title
Python-Based-Structure-Generate
# a,b,c,alpha,beta,gamma
%9.8f %9.8f %9.8f %6.3f %6.3f %6.3f\n''' %
(len_a, len_b, len_c, alpha, beta, gamma))
f3.write('''\n# nsp: Number of species
%i\n''' % len(element))
f3.write('\n# symbol(1:nsp): Atom symbols\n')
for ele in element:
f3.write('%5s' % ele)
f3.write(
'\n\n# natsp0(1:nsp): Number of atoms for each species in the assymetric unit\n'
)
for Nele in Nelement:
f3.write('%5i' % int(Nele))
f3.write(
'\n\n# coords0(1:nat0,1:3): Coordinates of each atom (one line per atom)\n'
)
for pos in position:
#print ('%8.7f %8.7f %8.7f' %(pos[1],pos[2],pos[3]))
f3.write('%8.7f %8.7f %8.7f\n' % (pos[1], pos[2], pos[3]))
f3.write('\n# na,nb,nc (supercell definition)\n')
for r in repeat:
f3.write('%3i' % int(r))
f3.write('\n\n# sptarget: Species to be substituted\n')
i = 1
for ele in element:
if ele == opts.target:
f3.write('%3i' % i)
i = i + 1
f3.write('\n\n# nsubs: Number of substitutions in the supercell\n%3i\n' %
opts.Nelement)
f3.write(
'''\n# newsymbol(1:2): Symbol of atom to be inserted in the selected position,
# symbol to be inserted in the rest of the positions for the same species.
%5s %5s\n''' % (opts.doping, opts.target))
# Ca Mg
f3.write('''
# FILER, MAPPER
# # FILER: 0 (no calc files generated), 1 (GULP), 2 (METADISE), 11 (VASP)
# # MAPPER: 0 (no mapping, use currect structure), >0 (map to structure in MAPTO file)
# # (each position in old structure is mapped to MAPPER positions in new structure)
11 0
''')
f3.close()
os.system('cd ' + path4 + '; bash ' + opts.sod)
def temp(opts):
i = 1
spli = []
fermi = []
unitcell, compound, position = jh.r_cryst_vasp(opts.poscar)
width, height = opts.figsize
xmin, xmax = opts.xlim
out = open("%s" % opts.outname, "w")
with os.popen("grep fermi %s |tail -1 | awk '{print $3}'" %
opts.outcar) as a:
temp = 1
for line in a:
if temp == 1:
fermi = line
temp = +1
else:
pass
out.write("python %s \\\n" % opts.vasp_dos)
out.write( " -y 0 %10.3f -z %8.5s --notot -q -s %i %i --fill -x %i %i \\"\
%( (unitcell[2][2] * opts.shift +2)/opts.dist ,\
fermi, \
width, height,\
# int(unitcell[2][2] / 2 / opts.dist),\
xmin, xmax\
))
out.write(
"\n -p 0 --pdosoffset=%f --lc=white --fac=%.2f --pdosoffset=%f -l '' \\"
% (opts.shift, opts.pdosFactor, opts.shift))
color = 'white'
for a in range(int(unitcell[2][2] / opts.dist) + 1):
temp = []
i = 1
speci = []
zzzzz = []
for x in position:
if x[3] > a * opts.dist - opts.overlap and \
x[3] < (a + 1) * opts.dist + opts.overlap:
temp.append(i)
zzzzz.append(x[3])
speci.append(x[0])
i += 1
speci.sort(reverse=True)
if sum(zzzzz) == 0: la = 0
else: la = sum(zzzzz) / len(zzzzz)
if len(speci) == 0:
color = 'white'
if la < unitcell[2][2] / 2 and opts.skip:
out.write(
"\n -p 0 --pdosoffset=%f --lc=white --fac=%.2f --pdosoffset=%f -l '' \\"
% (opts.shift, opts.pdosFactor, opts.shift))
if la > unitcell[2][2] / 2:
out.write(
"\n -p 0 --pdosoffset=%f --lc=white --fac=%.2f --pdosoffset=%f -l '' \\"
% (opts.shift, opts.pdosFactor, opts.shift))
else:
color = 'white'
out.write("\n -p '", )
for xx in temp:
out.write(" %s" % xx, )
out.write(" '", )
for x in opts.subele:
if x in speci: color = 'red'
if color != 'red':
for x in opts.ele2:
if x in speci:
color = 'blue'
if color != 'red' and color != 'blue':
for x in opts.ele1:
if x in speci:
color = 'black'
# if opts.element[0][0] in speci:
# if opts.element[0][1] in speci: color ='red'
# else: color ='black'
# elif opts.element[0][1] in speci: color ='blue'
# else:
# for c in opts.subelement[0]:
# if c in speci:
# color = 'red'
out.write(
" --lc=%s --fill --fac=%.2f --pdosoffset=%f -l " %
(color, opts.pdosFactor, opts.shift), )
for yy in set(speci):
out.write("%s" % yy)
out.write("_%.1f \\" % la)
if len(speci) == 0:
print 'Dividing slab with %.2f, In the %2i (th) layer, there is no element' % (
opts.dist, a)
else:
print 'Dividing slab with %.2f, In the %2i (th) layer, there is element:' % (
opts.dist, a), set(speci), 'as color of %s' % color
if opts.dosname:
out.write("\n --tofile %s" % (opts.dosname))
