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GenerateXsfFromEachOutcar_chinese.annotation.py
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#!/usr/bin/python
#encoding=utf-8
import os
import re
import copy
"""
This was used to automaticly produce *.xsf file for 1 ionic relaxation
Don't used for many ionic relaxation (eg: relax, AIMD and so on ). If you want do this ,please use get_xsf_from_total_md.py
gogal file name was current file name add .xsf
"""
__author__ = "Guanjie Wang"
__email__ = "[email protected]"
__date__ = "Oct. 1, 2017"
def new_vasp2force(OUTCARpath,number,gogal_path):
f = open(OUTCARpath, 'r')
data = []
max_types = 1
# 为了获得所有OUTCAR的configure、types和atoms
data.append(_scan_outcar_file(f))
configures = number
f.close()
#控制类型
max_types = max(max_types, len(data[-1][1]))
#控制原子数
natoms = sum(data[-1][2])
#对每一个进行下面操作
count = 0
#对元素种类操作
numbers=['0','1','2']
f = open(OUTCARpath, 'r')
#调用这一步的时候就会写入文件
total_number = _process_outcar_file_v5(OUTCARpath, f , natoms, count,data,max_types,configures,numbers,gogal_path)
f.close()
return natoms,total_number
def _scan_outcar_file(file_handle):
# first try TOTAL-FORCE
configs = 0
atom_types = []
titel = []
potcar = []
ipt = []
for line in file_handle:
if line.startswith('|'):
continue
if 'TOTAL-FORCE' in line:
configs += 1
if 'VRHFIN' in line:
atom_types.append(line.split()[1].replace('=','').replace(':',''))
if 'TITEL' in line:
titel.append(line.split()[3][0:2])
if 'ions per type' in line:
ipt = [int(s) for s in line.split()[4:]]
if 'POTCAR' in line:
potcar.append(line.split()[2][0:2])
if atom_types and ipt:
return [configs, atom_types, ipt]
if potcar and ipt:
return [configs,potcar,ipt]
exit('Could not determine atom types in file OUTCAR')
def _process_outcar_file_v5(OUTCARpath,f, natoms, count,data,max_types,configs,numbers,gogal_path):
total_number = 0
final_list = []
#循环OUTCAR
line = f.readline()
while line != '':
line = f.readline()
#迭代开始
if 'Iteration' in line:
energy = 0
box_x = []
box_y = []
box_z = []
stress = []
atom_data = []
#获取晶胞cell信息
if 'VOLUME and BASIS' in line:
for do in range(5):
line = f.readline()
box_x = [float(s) for s in line.replace('-',' -').split()[0:3]]
line = f.readline()
box_y = [float(s) for s in line.replace('-',' -').split()[0:3]]
line = f.readline()
box_z = [float(s) for s in line.replace('-',' -').split()[0:3]]
#获得压强信息
if 'in kB' in line:
stress = [float(s)/1602 for s in line.split()[2:8]]
#获得力学信息
if 'TOTAL-FORCE' in line:
count += 1
line = f.readline()
adata = [0] * 7
for num in range(len(data[-1][2])):
for k in range(data[-1][2][num]):
line = [float(s) for s in f.readline().split()[0:6]]
if not 1:
adata[0] = int(types[data[-1][1][num]])
else:
adata[0] = int(num)
adata[1] = float(line[0])
adata[2] = float(line[1])
adata[3] = float(line[2])
adata[4] = float(line[3])
adata[5] = float(line[4])
adata[6] = float(line[5])
atom_data.append(copy.copy(adata))
#获得能量信息
if 'energy without' in line:
#可以修改能量
energy = float(line.split()[6])
#获得能量信息之后表示本次迭代结束，开始输出
if str(count) in configs:
total_number += 1
penult_list = []
a1 = "#N %s 1" % natoms
a2 = "#C"
if not 1:
print(" %s" % numbers[0])
for j in range(1, max_types):
print(' %s' % numbers[j])
else:
a2 += " %s" % data[-1][1][0]
for j in range(1, max_types):
a2 += ' %s' % data[-1][1][j]
a3 = "## force file generated from file {0} config {1}".format(OUTCARpath, count)
a4 = "#X {0:13.8f} {1:13.8f} {2:13.8f}".format(box_x[0], box_x[1], box_x[2])
a5 = "#Y {0:13.8f} {1:13.8f} {2:13.8f}".format(box_y[0], box_y[1], box_y[2])
a6 = "#Z {0:13.8f} {1:13.8f} {2:13.8f}".format(box_z[0], box_z[1], box_z[2])
weight = 1.0
a7 = "#W {0:f}".format(weight)
a8 = "#E {0:.10f}".format(energy)
a9 = "#S"
if stress:
for num in range(6):
a9 += ' {0:8.7g}'.format(stress[num])
a10 = "#F"
penult_list.append(a1)
penult_list.append(a2)
penult_list.append(a3)
penult_list.append(a4)
penult_list.append(a5)
penult_list.append(a6)
penult_list.append(a7)
penult_list.append(a8)
penult_list.append(a9)
penult_list.append(a10)
for adata in atom_data:
b ="{0} {1:11.7g} {2:11.7g} {3:11.7g} {4:11.7g} {5:11.7g} {6:11.7g}".format(
adata[0], adata[1], adata[2], adata[3], adata[4], adata[5], adata[6])
penult_list.append(b)
final_list.append(penult_list)
_write_generate(gogal_path,count,penult_list,str(energy))
if total_number /100.0 == 0:
print("Have writen {0} xsf files".format(total_number))
if str(count) == configs[-1]:
break
if len(final_list) == len(configs):
final_dict = dict(zip(configs,final_list))
return total_number
else:
print("\033[0;33mWaring!!! Breaking!!! Beyond range")
print("Waring: total configure are {0}, but you input were {1}".format(count,configs[-1]))
print("\033[0;36mHave writen {0} xsf files\033[0m".format(total_number))
return total_number
def _write_generate(gogal_path,count,force_list,ene_str):
content = []
three_main_line = _get_line(force_list)
fir = ene_str.replace(' ', '')
firstline = '#total energy = ' + fir + ' eV' + '\n'
content.append(firstline)
secondline = '\n'
content.append(secondline)
thirdline = 'CRYSTAL\n'
content.append(thirdline)
fourthline = 'PRIMVEC\n'
content.append(fourthline)
fifthline = three_main_line[0]
content.append(fifthline)
sixthline = 'PRIMCOORD\n'
content.append(sixthline)
seventhline = three_main_line[1]
content.append(seventhline)
eighthline = three_main_line[2]
content.append(eighthline)
for x in range(0, len(content)):
if not isinstance(content[x], list):
open(gogal_path, 'a').write(content[x])
else:
for m in range(0, len(content[x])):
open(gogal_path, 'a').write(content[x][m])
#该函数严格依赖vasp2force生成的force文件
def _get_line(force_list):
line = force_list
atomic_coordinate = []
position_force = []
seven = ''
number = 0
#得到X,Y,Z的坐标，返回列表
for i in range(0,len(line)):
if i == 0:
atomic_num = re.findall(r'\d+',line[i])
seven = atomic_num[0]+' '+atomic_num[1]+'\n'
elif i == 1:
elements = re.findall(r'#C(.*)',line[i])[0].split()
elif i >= 3 and i <=5:
fif = re.findall(r'#[A-Z](.*)',line[i])
atomic_coordinate.append(fif[0]+'\n')
elif len(re.findall(r'F',line[i])) >0:
number = i+1
break
#将0,1,2 替换为元素符号，最多支持三个元素
#并将所有的每一行返回一个列表
for x in range(number,len(line)):
every_line = line[x].split()
if every_line[0] == '0':
line[x] = line[x].replace('0',elements[0],1)
elif every_line[0] == '1':
line[x] = line[x].replace('1',elements[1],1)
elif every_line[0] == '2':
line[x] = line[x].replace('2',elements[2],1)
position_force.append(line[x]+'\n')
#print('Atomic position and force total are %d rows. This shoule equal to atomic numbers '%len(position_force))
return atomic_coordinate,seven,position_force
def get_path(work_path):
work_file = os.listdir(work_path)
for i in work_file:
if re.findall(r'OUTCAR',i):
outcarpath = os.path.join(work_path,i)
return outcarpath
def _pri_center(content,num=58):
print(' ' * 15 + '|' + content.center(num, ' ') + '|' + ' ' * 15)
def main(path,gogal_path):
OUTCARpath = get_path(path)
control_number = ['1']
new_vasp2force(OUTCARpath,control_number,gogal_path)
print('\033[0;32m{0} \033[0mhas generated'.format(gogal_path.split('/')[-1]))
if __name__ == "__main__":
path = os.getcwd()
gogal_path = os.path.join(path, path.split('/')[-1] + '.xsf')
main(path,gogal_path)