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multiplayer1.py
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#!/bin/python
# -*- coding:utf-8 -*-
"""
@author: XueFeiLiu([email protected]),Nxu
@file: multiplayer.py
@time: 2019/1/29 21:44
A script to produce multi-layers of POSCAR
"""
import os
from numpy import *
import numpy as np
import shutil
import pprint
class VASP(object):
def __init__(self,layers,layerdistance,mode,lata=2.178,latb=2.178,disp_n=200000000000,disp_flag=True,agl=30):
self.lattice=np.zeros((3,3))
self.Selective_infomation=False
self.Direct_mode=True
#self.mode=mode0
self.mode0=mode
self.layers=layers # layers
self.layerdistance=layerdistance
self.displace=disp_n
self.flag_displace=disp_flag
self.rotate0=mat([[cos((agl/360)*2*np.pi),sin((agl/360)*2*np.pi),0],[-sin((agl/360)*2*np.pi),cos((agl/360)*2*np.pi),0],[0,0,1]])
self.M=self.rotate0
self.rotate1=mat([[cos((-agl/360)*2*np.pi),sin((-agl/360)*2*np.pi),0],[-sin((-agl/360)*2*np.pi),cos((-agl/360)*2*np.pi),0],[0,0,1]])
self.M1=self.rotate1
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!')
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!")
self.total_atom=sum(self.element_amount)
self.atomic_position=np.zeros((self.total_atom,3))
self.Selective_TF=[]
if self.Selective_infomation == True:
for i in range(self.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(self.total_atom):
line_tmp=poscar.readline()
self.atomic_position[i]=np.array([float(j) for j in line_tmp.split()[0:3]])
self.atomic_position*=self.scaling_factor
if self.Direct_mode == True:
self.cartesian_position=np.dot(self.atomic_position,self.lattice)
self.direct_position=self.atomic_position
else:
self.cartesian_position=self.atomic_position
self.direct_position=np.dot(self.atomic_position,np.linalg.inv(self.lattice))
poscar.close()
return (self.cartesian_position,self.direct_position)
def xyz_write(self):
print('Now writing new vasp structures.')
if os.path.exists("POSCAR1"):
shutil.copyfile("POSCAR1","POSCAR2")
os.remove("POSCAR1")
writen_lines=[]
writen_lines.append(self.title)
writen_lines.append(str(self.scaling_factor))
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")
if self.mode0.upper().startswith('C'):
writen_lines.append("Cartesian")
position_to_be_writen=self.cartesian_position
else:
writen_lines.append("Direct")
position_to_be_writen=self.direct_position
position_to_be_writen/=self.scaling_factor
if self.Selective_infomation == True:
for i in range(np.size(position_to_be_writen,0)):
writen_lines.append("{0:>15.8f}{1:>15.8f}{2:>15.8f} {3:4}{4:4}{5:4}" \
.format(position_to_be_writen[i][0],position_to_be_writen[i][1], \
position_to_be_writen[i][2],self.Selective_TF[i][0],\
self.Selective_TF[i][1],self.Selective_TF[i][2]))
else:
for i in range(np.size(position_to_be_writen,0)):
writen_lines.append("{0:>15.8f}{1:>15.8f}{2:>15.8f}" \
.format(position_to_be_writen[i][0],position_to_be_writen[i][1],
position_to_be_writen[i][2]))
writen_lines=[j+'\n' for j in writen_lines]
poscar=open("POSCAR1",'w')
poscar.writelines(writen_lines)
poscar.close()
def energy_extract(self):
print('Now reading vasp energies.')
if os.path.exists("OUTCAR"):
outcar=open("OUTCAR",'r')
for index,line in enumerate(outcar):
if "energy(sigma->0)" in line:
E0=float(line.split()[-1])
outcar.close()
self.energy=E0
return E0
elif os.path.exists("OSZICAR"):
oszicar=open("OSZICAR",'r')
for index,line in enumerate(oszicar):
if "E0=" in line:
E0=float(line.split()[4])
oszicar.close()
self.energy=E0
return E0
else:
raise IOError('OSZICAR OR OUTCAR does not exist！')
def multilayer(self):
print('Now produce new multi layers vasp structures.')
if os.path.exists("POSCAR_mullayer"+str(self.layers)):
shutil.copyfile("POSCAR_mullayer"+str(self.layers),"POSCAR_mullayer"+str(self.layers)+".bak")
os.remove("POSCAR_mullayer"+str(self.layers))
writen_lines=[]
writen_all_layers=[]
writen_each_layers=[]
writen_lines.append(self.title)
writen_lines.append(str(self.scaling_factor))
self.lattice[2][2]+=self.layerdistance*(self.layers-1)/self.scaling_factor
self.lattice_a=sqrt(self.lattice[0][0]**2+self.lattice[0][1]**2+self.lattice[0][2]**2)
self.lattice_b=sqrt(self.lattice[1][0]**2+self.lattice[1][1]**2+self.lattice[1][2]**2)
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))
self.element_amount0=self.element_amount[:]
self.element_amount=[self.element_amount0[i]*self.layers for i in range(len(self.element_amount0))]
writen_lines.append(' '+' '.join([str(j) for j in self.element_amount]))
if self.Selective_infomation == True:
writen_lines.append("Selective")
if self.mode0.upper().startswith('C'):
writen_lines.append("Cartesian")
position_to_be_writen=self.cartesian_position
else:
writen_lines.append("Direct")
position_to_be_writen=self.direct_position
position_to_be_writen/=self.scaling_factor
if self.Selective_infomation == True:
if self.mode0.upper().startswith('D'):
for i in range(np.size(position_to_be_writen,0)):
position_to_be_writen[i][2]-=(self.layers-1)*self.layerdistance/self.scaling_factor/2/self.lattice[2][2]
else:
pass
for num_layer in range(self.layers):
if num_layer < 1:
for i in range(np.size(position_to_be_writen,0)):
if self.mode0.upper().startswith('D'):
writen_all_layers.append("{0:>15.8f}{1:>15.8f}{2:>15.8f} {3:4}{4:4}{5:4}" \
.format(position_to_be_writen[i][0],position_to_be_writen[i][1], \
position_to_be_writen[i][2],self.Selective_TF[i][0],\
self.Selective_TF[i][1],self.Selective_TF[i][2]))
else:
writen_all_layers.append("{0:>15.8f}{1:>15.8f}{2:>15.8f} {3:4}{4:4}{5:4}" \
.format(position_to_be_writen[i][0],position_to_be_writen[i][1], \
position_to_be_writen[i][2],self.Selective_TF[i][0],\
self.Selective_TF[i][1],self.Selective_TF[i][2]))
else:
if self.flag_displace == True:
for i in range(np.size(position_to_be_writen,0)):
if self.mode0.upper().startswith('D'):
position_xyz=mat(position_to_be_writen[i])*self.M
position_to_be_writen[i]=position_xyz
position_to_be_writen[i][0]+=self.lattice_a/self.displace/self.scaling_factor
position_to_be_writen[i][1]+=self.lattice_b/self.displace/self.scaling_factor
position_to_be_writen[i][2]+=num_layer*self.layerdistance/self.scaling_factor/self.lattice[2][2]
writen_all_layers.append("{0:>15.8f}{1:>15.8f}{2:>15.8f} {3:4}{4:4}{5:4}" \
.format(position_to_be_writen[i][0],position_to_be_writen[i][1], \
position_to_be_writen[i][2],self.Selective_TF[i][0],\
self.Selective_TF[i][1],self.Selective_TF[i][2]))
position_to_be_writen[i][2]-=num_layer*self.layerdistance/self.scaling_factor/self.lattice[2][2]
else:
position_xyz=mat(position_to_be_writen[i])*self.M
position_to_be_writen[i]=position_xyz
position_to_be_writen[i][0]+=self.lattice_a/self.displace/self.scaling_factor
position_to_be_writen[i][1]+=self.lattice_b/self.displace/self.scaling_factor
position_to_be_writen[i][2]+=num_layer*self.layerdistance/self.scaling_factor
writen_all_layers.append("{0:>15.8f}{1:>15.8f}{2:>15.8f} {3:4}{4:4}{5:4}" \
.format(position_to_be_writen[i][0],position_to_be_writen[i][1], \
position_to_be_writen[i][2],self.Selective_TF[i][0],\
self.Selective_TF[i][1],self.Selective_TF[i][2]))
position_to_be_writen[i][2]-=num_layer*self.layerdistance/self.scaling_factor
self.flag_displace = False
else:
for i in range(np.size(position_to_be_writen,0)):
if self.mode0.upper().startswith('D'):
position_xyz=mat(position_to_be_writen[i])*self.M1
position_to_be_writen[i]=position_xyz
position_to_be_writen[i][0]-=self.lattice_a/self.displace/self.scaling_factor
position_to_be_writen[i][1]-=self.lattice_b/self.displace/self.scaling_factor
position_to_be_writen[i][2]+=num_layer*self.layerdistance/self.scaling_factor/self.lattice[2][2]
writen_all_layers.append("{0:>15.8f}{1:>15.8f}{2:>15.8f} {3:4}{4:4}{5:4}" \
.format(position_to_be_writen[i][0],position_to_be_writen[i][1], \
position_to_be_writen[i][2],self.Selective_TF[i][0],\
self.Selective_TF[i][1],self.Selective_TF[i][2]))
position_to_be_writen[i][2]-=num_layer*self.layerdistance/self.scaling_factor/self.lattice[2][2]
else:
position_xyz=mat(position_to_be_writen[i])*self.M1
position_to_be_writen[i]=position_xyz
position_to_be_writen[i][0]-=self.lattice_a/self.displace/self.scaling_factor
position_to_be_writen[i][1]-=self.lattice_b/self.displace/self.scaling_factor
position_to_be_writen[i][2]+=num_layer*self.layerdistance/self.scaling_factor
writen_all_layers.append("{0:>15.8f}{1:>15.8f}{2:>15.8f} {3:4}{4:4}{5:4}" \
.format(position_to_be_writen[i][0],position_to_be_writen[i][1], \
position_to_be_writen[i][2],self.Selective_TF[i][0],\
self.Selective_TF[i][1],self.Selective_TF[i][2]))
position_to_be_writen[i][2]-=num_layer*self.layerdistance/self.scaling_factor
self.flag_displace = True
writen_all_layers=[j+'\n' for j in writen_all_layers]
writen_each_layers=[writen_all_layers[k:k+self.total_atom] for k in range(0,len(writen_all_layers),self.total_atom)]
else:
if self.mode0.upper().startswith('D'):
for i in range(np.size(position_to_be_writen,0)):
position_to_be_writen[i][2]-=(self.layers-1)*self.layerdistance/self.scaling_factor/2/self.lattice[2][2]
else:
pass
for num_layer in range(self.layers):
if num_layer < 1:
for i in range(np.size(position_to_be_writen,0)):
if self.mode0.upper().startswith('D'):
position_to_be_writen[i][2]+=num_layer*self.layerdistance/self.scaling_factor/self.lattice[2][2]
writen_all_layers.append("{0:>15.8f}{1:>15.8f}{2:>15.8f}" \
.format(position_to_be_writen[i][0],position_to_be_writen[i][1],position_to_be_writen[i][2]))
position_to_be_writen[i][2]-=num_layer*self.layerdistance/self.scaling_factor/self.lattice[2][2]
else:
position_to_be_writen[i][2]+=num_layer*self.layerdistance/self.scaling_factor
writen_all_layers.append("{0:>15.8f}{1:>15.8f}{2:>15.8f}" \
.format(position_to_be_writen[i][0],position_to_be_writen[i][1],position_to_be_writen[i][2]))
position_to_be_writen[i][2]-=num_layer*self.layerdistance/self.scaling_factor
else:
if self.flag_displace == True:
for i in range(np.size(position_to_be_writen,0)):
if self.mode0.upper().startswith('D'):
position_xyz=mat(position_to_be_writen[i])*self.M
position_to_be_writen[i]=position_xyz
position_to_be_writen[i][0]+=self.lattice_a/self.displace/self.scaling_factor
position_to_be_writen[i][1]+=self.lattice_b/self.displace/self.scaling_factor
position_to_be_writen[i][2]+=num_layer*self.layerdistance/self.scaling_factor/self.lattice[2][2]
writen_all_layers.append("{0:>15.8f}{1:>15.8f}{2:>15.8f}" \
.format(position_to_be_writen[i][0],position_to_be_writen[i][1],position_to_be_writen[i][2]))
position_to_be_writen[i][2]-=num_layer*self.layerdistance/self.scaling_factor/self.lattice[2][2]
else:
position_xyz=mat(position_to_be_writen[i])*self.M
position_to_be_writen[i]=position_xyz
position_to_be_writen[i][0]+=self.lattice_a/self.displace/self.scaling_factor
position_to_be_writen[i][1]+=self.lattice_b/self.displace/self.scaling_factor
position_to_be_writen[i][2]+=num_layer*self.layerdistance/self.scaling_factor
writen_all_layers.append("{0:>15.8f}{1:>15.8f}{2:>15.8f}" \
.format(position_to_be_writen[i][0],position_to_be_writen[i][1],position_to_be_writen[i][2]))
position_to_be_writen[i][2]-=num_layer*self.layerdistance/self.scaling_factor
self.flag_displace = False
else:
for i in range(np.size(position_to_be_writen,0)):
if self.mode0.upper().startswith('D'):
position_xyz=mat(position_to_be_writen[i])*self.M1
position_to_be_writen[i]=position_xyz
position_to_be_writen[i][0]-=self.lattice_a/self.displace/self.scaling_factor
position_to_be_writen[i][1]-=self.lattice_b/self.displace/self.scaling_factor
position_to_be_writen[i][2]+=num_layer*self.layerdistance/self.scaling_factor/self.lattice[2][2]
writen_all_layers.append("{0:>15.8f}{1:>15.8f}{2:>15.8f}" \
.format(position_to_be_writen[i][0],position_to_be_writen[i][1],position_to_be_writen[i][2]))
position_to_be_writen[i][2]-=num_layer*self.layerdistance/self.scaling_factor/self.lattice[2][2]
else:
position_xyz=mat(position_to_be_writen[i])*self.M1
position_to_be_writen[i]=position_xyz
position_to_be_writen[i][0]-=self.lattice_a/self.displace/self.scaling_factor
position_to_be_writen[i][1]-=self.lattice_b/self.displace/self.scaling_factor
position_to_be_writen[i][2]+=num_layer*self.layerdistance/self.scaling_factor
writen_all_layers.append("{0:>15.8f}{1:>15.8f}{2:>15.8f}" \
.format(position_to_be_writen[i][0],position_to_be_writen[i][1],position_to_be_writen[i][2]))
position_to_be_writen[i][2]-=num_layer*self.layerdistance/self.scaling_factor
self.flag_displace = True
writen_all_layers=[j+'\n' for j in writen_all_layers]
#pprint.pprint(writen_all_layers)
writen_each_layers=[writen_all_layers[k:k+self.total_atom] for k in range(0,len(writen_all_layers),self.total_atom)]
#pprint.pprint(writen_each_layers)
writen_lines=[j+'\n' for j in writen_lines]
poscar=open("POSCAR_mullayer"+str(self.layers),'w')
poscar.writelines(writen_lines)
j=0
#print(self.element_amount0)
for i in self.element_amount0:
for num_layer in range(self.layers):
poscar.writelines(writen_each_layers[num_layer][j:j+i])
j+=i
poscar.close()
if __name__ == "__main__":
a=str("Given the number of layers ,distance beween two layers and type of atoms coordination you want to build:\n")
words=len(a)
print("*"*words)
print(a)
print("*"*words)
#n_layer,ldistance=input("Input the number of layers and distance:\n")
n_layer=int(input("Input the number of layers:\n"))
ldistance=float(input("Input the distance of two layers:\n"))
coordtype=str(input("Input the type of atoms coordination(C or D):\n"))
angle0=float(input("Input the angle you want to rotate:\n"))
distance_n=float(input("Input the displace number according to supercell:\n"))
poscar=VASP(layers=n_layer,layerdistance=ldistance,mode=coordtype,agl=angle0,disp_n=distance_n)
cartesian_position,direct_position=poscar.xyz_read()
#print(cartesian_position)
poscar.multilayer()