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resort.py
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resort.py
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#!/bin/python
# -*- coding:utf-8 -*-
import os
import numpy as np
import shutil
class VASP(object):
def __init__(self):
self.lattice=np.zeros((3,3))
self.Selective_infomation=False
self.Direct_mode=True
def xyz_read(self):
print('Now reading vasp structures.')
if os.path.exists("POSCAR"):
poscar=open("POSCAR",'r')
elif os.path.exists("CONTCAR"):
poscar=open("CONTCAR",'r')
else:
raise IOError('CONTCAR OR POSCAR does not exist！')
self.title=poscar.readline().rstrip('\r\n').rstrip('\n')
self.scaling_factor=float(poscar.readline())
for i in range(3):
self.lattice[i]=np.array([float(j) for j in poscar.readline().split()])
self.lattice*=self.scaling_factor
self.element_list=[j for j in poscar.readline().split()]
try:
self.element_amount=[int(j) for j in poscar.readline().split()]
except ValueError:
raise ValueError('VASP 5.x POSCAR is needed!')
self.all_element=[]
for i in range(len(self.element_list)):
self.all_element.extend([self.element_list[i]]*self.element_amount[i] )
#print(self.all_element)
line_tmp=poscar.readline()
if line_tmp.strip().upper().startswith("S"):
self.Selective_infomation=True
line_tmp=poscar.readline()
else:# no atoms fixed
self.Selective_infomation=False
if line_tmp.strip().upper().startswith("D"):
self.Direct_mode=True
elif line_tmp.strip().upper().startswith("C"):
self.Direct_mode=False
else:
raise ValueError("POSCAR format is not correct!")
total_atom=sum(self.element_amount)
self.atomic_position=np.zeros((total_atom,3))
self.Selective_TF=[]
if self.Selective_infomation == True:
for i in range(total_atom):
line_tmp=poscar.readline()
self.atomic_position[i]=np.array([float(j) for j in line_tmp.split()[0:3]])
self.Selective_TF.append([j for j in line_tmp.split()[3:]])
else:
for i in range(total_atom):
line_tmp=poscar.readline()
self.atomic_position[i]=np.array([float(j) for j in line_tmp.split()[0:3]])
if self.Direct_mode == True:
self.atomic_position=np.dot(self.atomic_position,self.lattice)
#self.atomic_position*=self.scaling_factor
poscar.close()
return self.atomic_position
def xyz_write(self):
print('Now writing new vasp structures.')
if os.path.exists("POSCAR-bak"):
shutil.copyfile("POSCAR-bak","POSCAR-bak1")
os.remove("POSCAR-bak")
writen_lines=[]
writen_lines.append(self.title)
writen_lines.append('1.0')
for i in range(3):
writen_lines.append("{0:>15.8f}{1:>15.8f}{2:>15.8f}" \
.format(self.lattice[i][0],self.lattice[i][1],self.lattice[i][2]))
writen_lines.append(' '+' '.join(self.element_list))
writen_lines.append(' '+' '.join([str(j) for j in self.element_amount]))
if self.Selective_infomation == True:
writen_lines.append("Selective")
writen_lines.append("Cartesian")
if self.Selective_infomation == True:
for i in range(np.size(self.atomic_position,0)):
writen_lines.append("{0:>15.8f}{1:>15.8f}{2:>15.8f} {3:4}{4:4}{5:4}" \
.format(self.atomic_position[i][0],self.atomic_position[i][1], \
self.atomic_position[i][2],self.Selective_TF[i][0],\
self.Selective_TF[i][1],self.Selective_TF[i][2]))
else:
for i in range(np.size(self.atomic_position,0)):
writen_lines.append("{0:>15.8f}{1:>15.8f}{2:>15.8f}" \
.format(self.atomic_position[i][0],self.atomic_position[i][1], \
self.atomic_position[i][2]))
writen_lines=[j+'\n' for j in writen_lines]
poscar=open("POSCAR-bak",'w')
poscar.writelines(writen_lines)
poscar.close()
def determinelayers(z_cartesian):
seq = sorted(z_cartesian)
min = seq[0]
layerscount = {}
sets = [min]
for j in range(len(seq)):
if abs(seq[j]-min) >= thresthold:
min = seq[j]
sets.append(min)
for i in range(1,len(sets)+1):
layerscount[i] = []
if i > 1:
for k in range(len(z_cartesian)):
if abs(z_cartesian[k]-sets[i-1]) <= thresthold and not abs(z_cartesian[k]-sets[i-2]) <=thresthold:
layerscount[i].append(k)
else:
for k in range(len(z_cartesian)):
if abs(z_cartesian[k]-sets[i-1]) <= thresthold:
layerscount[i].append(k)
return layerscount
if __name__ == "__main__":
thresthold=1.5 #A
poscar=VASP()
cartesian_position=poscar.xyz_read()
substitute_elements= [ 'Xe', 'La', 'Pr', 'Nd', 'Pm', 'Sm', \
'Eu', 'Gd', 'Tb', 'Dy', 'Ho', 'Er', 'Tm', 'Yb', 'Lu',\
'Tl', 'Bi', 'Po', 'At', 'Rn', 'Fr', 'Ra', 'Ac',\
'Th', 'Pa', 'Np', 'Pu', 'Am', 'Cm', 'Bk', 'Cf', \
'Es', 'Fm', 'Md', 'No', 'Lr']
layerscount =determinelayers(cartesian_position[:,2].tolist())
#print(layerscount)
import sys
if sys.version[0]=='2':
input=raw_input
fixedlayer = int(input("Found %d layers, choose how many layers want to substitute with various elements------>" %len(layerscount)))
index=0
new_element=[]
new_element_index=[]
for i in range(1,len(layerscount)+1):
if i <= fixedlayer:
old_element=[poscar.all_element[m] for m in layerscount[i]]
unique_element=list(set(old_element))
for n in unique_element:
new_element.append(substitute_elements[index])
index+=1
tmp=[]
for index_,l in enumerate(old_element):
if l==n:
tmp.append(layerscount[i][index_])
new_element_index.append(tmp)
else:
new_element.append(poscar.all_element[layerscount[i][0]])
new_element_index.append(layerscount[i])
old_atomic_position=cartesian_position.copy()
poscar.element_list=new_element
poscar.element_amount=[len(i) for i in new_element_index]
index=0
#print(new_element_index)
for i in new_element_index:
for j in i:
poscar.atomic_position[index]= old_atomic_position[j]
index+=1
poscar.xyz_write()