/
lattice_check.py
137 lines (122 loc) · 5.12 KB
/
lattice_check.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
# Getting lattice parameters
import os
import pymatgen as pmg
def lattice_check(model,structure,li_concentration,functional_list,U_value,conf):
if (model == 'Li2MnO3'):
dir = os.path.join('/scratch/antwerpen/204/vsc20412',model,model[0:2]+li_concentration+model[3:],structure)
elif (model == 'Li2IrO3'):
dir = os.path.join('/scratch/antwerpen/204/vsc20412',model,model[0:2]+li_concentration+model[3:])
elif (model == 'Li2MnSnO3'):
dir = os.path.join('/scratch/antwerpen/204/vsc20412',model,'Li'+li_concentration)
try:
if (len(U_value)>1):
values = U_value
except:
values = [U_value]
if functional_list == 'pbeU':
h=len(values)
w=4
lattice_parameters_length = [[0 for x in range(w)] for y in range(h)]
for i in range(0,3):
q=0
for u in values:
directory=os.path.join(dir,"conf_"+str(conf), 'pbeU',str(u)) # <--- Specify U-vaule (last number) or dir for SCAN and HSE06
os.chdir(directory)
s = pmg.Structure.from_file('CONTCAR')
lattice_parameters_length[q][i+1]=s.lattice.abc[i]
lattice_parameters_length[q][0]=u
q = q + 1
elif functional_list == 'scan':
h=1
w=4
lattice_parameters_length = [[0 for x in range(w)] for y in range(h)]
try:
directory=os.path.join(dir,"conf_"+str(conf), 'scan') # <--- Specify U-vaule (last number) or dir for SCAN and HSE06
os.chdir(directory)
s = pmg.Structure.from_file('CONTCAR')
for i in range(0,3):
lattice_parameters_length[0][i+1]=s.lattice.abc[i]
except:
pass
elif functional_list == 'hse':
h=1
w=4
lattice_parameters_length = [[0 for x in range(w)] for y in range(h)]
try:
directory=os.path.join(dir,"conf_"+str(conf), 'hse') # <--- Specify U-vaule (last number) or dir for SCAN and HSE06
os.chdir(directory)
s = pmg.Structure.from_file('CONTCAR')
for i in range(0,3):
lattice_parameters_length[0][i+1]=s.lattice.abc[i]
except:
pass
elif functional_list == ("pbeU", "scan" , "hse"):
h=len(values)+2
w=4
lattice_parameters_length = [[0 for x in range(w)] for y in range(h)]
#pbeu part
try:
if (len(U_value)>1):
values = U_value
except:
values = [U_value]
for i in range(0,3):
q=0
for u in values:
directory=os.path.join(dir,"conf_"+str(conf), 'pbeU',str(u)) # <--- Specify U-vaule (last number) or dir for SCAN and HSE06
os.chdir(directory)
s = pmg.Structure.from_file('CONTCAR')
lattice_parameters_length[q][i+1]=s.lattice.abc[i]
lattice_parameters_length[q][0]=u
q = q + 1
try:
#scan part
directory=os.path.join(dir,"conf_"+str(conf), 'scan') # <--- Specify U-vaule (last number) or dir for SCAN and HSE06
os.chdir(directory)
s = pmg.Structure.from_file('CONTCAR')
for i in range(0,3):
lattice_parameters_length[q][i+1]=s.lattice.abc[i]
except:
pass
#hse part
try:
directory=os.path.join(dir,"conf_"+str(conf), 'hse') # <--- Specify U-vaule (last number) or dir for SCAN and HSE06
os.chdir(directory)
s = pmg.Structure.from_file('CONTCAR')
for i in range(0,3):
lattice_parameters_length[q+1][i+1]=s.lattice.abc[i]
except:
pass
elif functional_list == ("pbeU", "scan"):
h=len(values)+1
w=4
lattice_parameters_length = [[0 for x in range(w)] for y in range(h)]
#pbeu part
try:
if (len(U_value)>1):
values = U_value
except:
values = [U_value]
for i in range(0,3):
q=0
for u in values:
directory=os.path.join(dir,"conf_"+str(conf), 'pbeU',str(u)) # <--- Specify U-vaule (last number) or dir for SCAN and HSE06
os.chdir(directory)
s = pmg.Structure.from_file('CONTCAR')
lattice_parameters_length[q][i+1]=s.lattice.abc[i]
lattice_parameters_length[q][0]=u
q = q + 1
try:
#scan part
directory=os.path.join(dir,"conf_"+str(conf), 'scan') # <--- Specify U-vaule (last number) or dir for SCAN and HSE06
os.chdir(directory)
s = pmg.Structure.from_file('CONTCAR')
for i in range(0,3):
lattice_parameters_length[q][i+1]=s.lattice.abc[i]
except:
pass
else:
pass
header = ("U-value (eV)", 'a-lattice (A)', 'b-lattice (A)','c-lattice (A)')
return (header,lattice_parameters_length)
#return tabulate(lattice_parameters_length, headers=header, tablefmt="latex", floatfmt=(".1f",".5f"))