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
|
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Abinit Post Process Application
author: Martin Alexandre
last edited: May 2013
"""
import commands
class Input:
# This class can read input file for APPA
# This is useful for run the no windozs version of APPA
#-----------------------------#
#-------CONSTRUCTOR-----------#
#-----------------------------#
def __init__(self, pnamefile):
self.input_file = str(pnamefile)
#-----------------------------#
#-----------METHODS-----------#
#-----------------------------#
def read(self):
try:
import re
re_lib = True
except:
re_lib = False
if re_lib :
return self.expression_regular()
def expression_regular(self):
import re
input = {}
file = open(self.input_file)
for line in file:
#Remove the comment line
m = re.search('^\s*#.*', line)
if m:
continue
m = re.search('^\s*$', line)
if m:
continue
m = re.search('^\s*file\s+(\S+)', line)
if m:
file = m.group(1)
input[m.group(1)] = {}
continue
m = re.search('^\s*stepmin\s+(\S+)', line)
if m:
input[file]["stepmin"] = m.group(1)
continue
m = re.search('^\s*stepmax\s+(\S+)', line)
if m:
input[file]["stepmax"] = m.group(1)
continue
m = re.search('^\s*potential_energy\s+(\S*)\s*', line)
if m:
if m.group(1):
input[file]['potential_energy'] = m.group(1)
else:
input[file]['potential_energy'] = 3
continue
m = re.search('^\s*total_energy\s+(\S*)\s*', line)
if m:
if m.group(1):
input[file]['total_energy'] = m.group(1)
else:
input[file]['total_energy'] = 3
continue
m = re.search('^\s*kinetic_energy\s+(\S*)\s*', line)
if m:
if m.group(1):
input[file]['kinetic_energy'] = m.group(1)
else:
input[file]['kinetic_energy'] = 3
continue
m = re.search('^\s*pressure\s+(\S*)\s*', line)
if m:
if m.group(1):
input[file]['pressure'] = m.group(1)
else:
input[file]['pressure'] = 3
continue
m = re.search('^\s*temperature\s+(\S*)\s*', line)
if m:
if m.group(1):
input[file]['temperatures'] = m.group(1)
else:
input[file]['temperatures'] = 3
continue
m = re.search('^\s*vacf\s+(\S*)\s*', line)
if m:
if m.group(1):
input[file]['vacf'] = m.group(1)
else:
input[file]['vacf'] = 3
continue
m = re.search('^\s*vdos\s+(\S*)\s*', line)
if m:
if m.group(1):
input[file]['vdos'] = m.group(1)
else:
input[file]['vdos'] = 3
continue
m = re.search('^\s*vdosres\s+(\S*)\s*', line)
if m:
if m.group(1):
input[file]['vdosres'] = m.group(1)
else:
input[file]['vdosres'] = 8
continue
m = re.search('^\s*stress\s+(\S*)\s*', line)
if m:
if m.group(1):
input[file]['stress'] = m.group(1)
else:
input[file]['stress'] = 3
continue
m = re.search('^\s*rdf\s+(\S*)\s*', line)
if m:
if m.group(1):
input[file]['rdf'] = m.group(1)
else:
input[file]['rdf'] = 8
continue
print "!!!Warning "+ line.replace('\n','')+ " is not a keyword"
return input
#temp = commands.getoutput(' grep \'*\' '+self.input_file+' | awk \'{print $1,$2}\' ')
#print temp
|
