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python-nebmaker.py
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python-nebmaker.py
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#!/usr/bin/python
#edit by [email protected]
#reference:http://blog.sina.com.cn/s/blog_b364ab230102wj0g.html
#2016/06/22
import numpy as np
import os
import time
step_init=0.0001
images=input("input num of images: ")
ininame=raw_input("ini structure: ")
finname=raw_input("fin structure: ")
#read ini structure
fileopen=open(ininame,'r')
ini_data=fileopen.readlines()
head=ini_data[:9]
atom_num=sum(map(int,head[6].split()))
ini_data=ini_data[9:9+atom_num]
tmp=[]
fix=[]
for i in range(atom_num):
tmp.append(map(float,ini_data[i].split()[0:3]))
if(ini_data[i].split()[4]=='F'): fix.append(1)
else: fix.append(0)
pos_a=np.array(tmp)
#read fin stucture
fileopen=open(finname,'r')
fin_data=fileopen.readlines()
fin_data=fin_data[9:9+atom_num]
tmp=[]
for i in fin_data:
tmp.append(map(float,i.split()[0:3]))
pos_b=np.array(tmp)
#correction of periodic boundary condition
for i in range(atom_num):
for j in range(3):
if(pos_a[i][j]-pos_b[i][j]>0.5): pos_a[i][j]-=1
if(pos_a[i][j]-pos_b[i][j]<-0.5): pos_b[i][j]-=1
#get dist matrix and linear interpolation
dist_a=np.zeros([atom_num,atom_num])
dist_b=np.zeros([atom_num,atom_num])
for i in range(atom_num):
for j in range(atom_num):
tmp_a=0
tmp_b=0
for k in range(3):
tmp_a+=(pos_a[i][k]-pos_a[j][k])**2
tmp_b+=(pos_b[i][k]-pos_b[j][k])**2
dist_a[i,j]=np.sqrt(tmp_a)
dist_b[i,j]=np.sqrt(tmp_b)
dist_im=np.zeros([images,atom_num,atom_num])
pos_im=np.zeros([images,atom_num,3])
for i in range(images):
dist_im[i]=dist_a+(i+1.0)*(dist_b-dist_a)/(images+1.0)
pos_im[i]=pos_a+(i+1.0)*(pos_b-pos_a)/(images+1.0)
#optimization using steepest descent method
pos_tmp=np.zeros([atom_num,3])
dist_tmp=np.zeros([atom_num,atom_num])
s0=np.zeros(images)
s1=np.zeros(images)
flag=np.zeros(images)
for im in range(images):
if(flag[im]==1): continue
step=step_init
print "generate image "+str(im+1)
loop=0
while(1):
for i in range(atom_num): #get dist_tmp
for j in range(atom_num):
if(i==j):
dist_tmp[i,j]=10
else:
tmp=0
for k in range(3):
tmp+=(pos_im[im][i][k]-pos_im[im][j][k])**2
dist_tmp[i,j]=np.sqrt(tmp)
for i in range(atom_num):
for sigma in range(3):
grad=0
for j in range(atom_num):
if(j!=i):
grad+=2*(dist_im[im][i][j]-dist_tmp[i][j])*(pos_im[im][i][sigma]-pos_im[im][j][sigma])\
*(2*dist_im[im][i][j]-dist_tmp[i][j])/dist_tmp[i,j]**5
pos_tmp[i][sigma]=pos_im[im][i][sigma]+step*grad
pos_im[im]=pos_tmp
#judge convergence
s0[im]=s1[im]
s1[im]=0
for i in range(atom_num):
for j in range(i):
s1[im]+=(dist_im[im][i][j]-dist_tmp[i][j])**2/dist_tmp[i][j]**4
loop+=1
print "loop:%d"%loop
if(abs(s0[im]-s1[im])<0.01):
print "Converged!"
flag[im]=1
break
if(loop>1 and s1[im]>s0[im]): step=step/3
#mkdir and generate poscar files
if(images+1<10): num='0'+str(images+1)
else: num=str(images+1)
os.system("mkdir 00")
os.system("cp %s 00/POSCAR" %ininame)
os.system("mkdir "+num)
os.system("cp "+finname+" "+num+"/POSCAR")
for i in range(images):
if(i+1<10): num='0'+str(i+1)
else: num=str(i+1)
os.system("mkdir "+num)
data=pos_im[i].tolist()
filename=num+"/POSCAR"
f=file(filename,"a+")
f.writelines(head)
for j in range(atom_num):
line=map(str,data[j])
line=" ".join(line)
if(fix[j]==1): line=line+' F F F\n'
else: line=line+' T T T\n'
f.write(line)
f.close()