-
Notifications
You must be signed in to change notification settings - Fork 1
/
Copy pathGenerateXsfFromTotalMd_chinese.annotation.py
296 lines (292 loc) · 11.4 KB
/
GenerateXsfFromTotalMd_chinese.annotation.py
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
#!/usr/bin/python
#encoding=utf-8
import os
import re
import shutil
import time
import copy
from optparse import OptionParser
"""
This was used to automaticly produce *.xsf file
Current path must have OUTCAR file
"""
__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 = []
ipt = []
potcar = []
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 = []
name = str(count).zfill(5) + '.xsf' #写个5位字符串，不足的补充0
name_path = os.path.join(gogal_path, name)
print('The present task is \033[0;32m{0}\033[0m th.'.format(count))
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(name_path, 'a').write(content[x])
else:
for m in range(0, len(content[x])):
open(name_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)
break
if outcarpath:
gogal_path = os.path.join(work_path,'gogal')
if os.path.exists(gogal_path):
print("The gogal path exits. Deleted")
time.sleep(1)
rm = 'yes'
if rm == 'yes':
shutil.rmtree(gogal_path)
os.mkdir(gogal_path)
else:
exit("Can't delete exit force!!! So the script must stop")
else:
os.mkdir(gogal_path)
return outcarpath,gogal_path
else:
exit("wrong! Don't find OUTCAR file")
def get_num(star,stop,space):
return [str(x) for x in range(int(star),int(stop)+1,int(space))]
def parse_option():
usage = "%prog -n arg1 eg:%prog -n 1,50000,10"
parse = OptionParser(usage)
parse.add_option('-n','--number',action='store',type='string',dest='num',default='1,50000,10',
help='''input star,stop,space number
\033[0;32meg: -n 1,50,5\033[0m means from 1 to 50 interval 5
default: star=1,stop=50000,space=10''',metavar='inter number')
(option,args) = parse.parse_args()
star,stop,space = option.num.split(',')
try:
return int(star),int(stop),int(space)
except ValueError:
exit('\033[0;31mValueError: please input inter number\033[0m')
def readme():
print(('-'*60).center(90))
_pri_center('This was used to automaticly produce *.xsf')
_pri_center("\033[0;35mNecessary\033[0m: VASP's OUTCAR file",69)
_pri_center('All *.XSF were stored in gogal file')
_pri_center('You can use -n input start stop and space to control')
print(('-'*60).center(90))
def _pri_center(content,num=58):
print(' ' * 15 + '|' + content.center(num, ' ') + '|' + ' ' * 15)
def tail(filenumbers,alltime,gogalpath):
print(('-' * 60).center(90))
_pri_center('Congratulation!!!!!')
_pri_center('You have successfully make \033[0;36m### %d ###\033[0m XSF files '% filenumbers,69)
_pri_center('*.XSF stored in gogal file')
_pri_center('\033[0;32mTime used was {0} s\033[0m'.format(alltime),69)
print(('-' * 60).center(90))
def main(path):
startime = time.time()
readme()
star, stop, space = parse_option()
OUTCARpath,gogal_path = get_path(path)
control_number = get_num(star,stop,space)
natoms,filenumbers = new_vasp2force(OUTCARpath,control_number,gogal_path)
alltime = time.time() - startime
tail(filenumbers,alltime,gogal_path)
if __name__ == "__main__":
path = os.getcwd()
main(path)