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 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
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,\
compound = new_compound, \
filename = output_name, \
unitcell = unitcell1, \
Selective = select)
t1 = time()
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)
#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,
filename='new.vasp',
unitcell=unitcell,
Selective=select)
t1 = time()
## 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]
])
new_unitcell.append([
unitcell[2][0], unitcell[2][1],
float(unitcell[2][2]) + float(sys.argv[4])
])
jh.w_poscar(position,
compound=compound,
filename=filename + '_new.vasp',
unitcell=new_unitcell,
Selective=False)
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', \
unitcell = unitcell, \
Selective = False)
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,
'Enmax': int(Enmax),
'Valency': int(Valency),
'AtomicMass': float(AtomicMass)
