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
|
#! /usr/bin/python
import os
import sys
import re
from string import *
from math import sqrt
leftpat=re.compile('([A-Z][a-z]?)([=+#@-])\.moi$')
rightpat=re.compile('([=+#@-])([A-Z][a-z]?)\.moi$')
centerpat=re.compile('([=+#@-])([A-Z][a-z]?)([=+#@-])\.moi$')
thetapat=re.compile(" *theta *= *([\d\.]+)")
parmpat = re.compile("([A-Z][a-z]?)([\+=\-@#])([A-Z][a-z]?) +Ks= *([\d\.]+) +R0= *([\d\.]+) +De= *([\d\.]+)")
commpat = re.compile("#")
pref="""! Gamess control file
$CONTRL SCFTYP=UHF MAXIT=200 RUNTYP=energy MULT=1 ICHARG=0
ICUT=9 ITOL=20 INTTYP=best COORD=zmt nprint=-5 $END
$SCF NCONV=5 dirscf=.t. DAMP=.t. SHIFT=.t. DIIS=.T. npunch=0 $END
$STATPT NSTEP=50 OPTTOL=0.0001 IFREEZ(1)=1,2,3 $END
$FORCE VIBANL=.f. PRTIFC=.f. $END
$SYSTEM TIMLIM=10000 MWORDS=250 $END
! $BASIS GBASIS=AM1 $END
$BASIS GBASIS=N31 NGAUSS=6 NDFUNC=1 NPFUNC=1 DIFFSP=.t. $END
$DFT DFTTYP=B3LYP $END
$DATA
*** bending for %s
C1
"""
angs=[('.1',-30),('.2',-20),('.3',-15),('.4',-7),('.5',0),
('.6',7),('.7',15),('.8',20),('.9',30)]
bontyp = {'-':'1', '=':'2', '+':'3','@':'a', '#':'g'}
Rzeros={}
f=open('stretch.parms')
for lin in f.readlines():
if commpat.match(lin): continue
m = parmpat.match(lin)
l,b,r = m.group(1),m.group(2),m.group(3)
ks,r0,de = map(lambda p: float(m.group(p)),[4,5,6])
Rzeros[l+b+r]=r0
Rzeros[r+b+l]=r0
lefts = []
rights = []
centers = []
for fn in os.listdir('moieties'):
if leftpat.match(fn): lefts += [fn]
if rightpat.match(fn): rights += [fn]
if centerpat.match(fn): centers += [fn]
### hack
rights = ['-B.moi']
for c in centers:
m=centerpat.match(c)
ce=m.group(2)
clb=m.group(1)
crb=m.group(3)
# print c
for l in lefts:
m=leftpat.match(l)
le=m.group(1)
lb=m.group(2)
if lb != clb: continue
# print l
for r in rights:
m=rightpat.match(r)
re=m.group(2)
rb=m.group(1)
if rb != crb: continue
# print r
name = le+lb+ce+rb+re
print name
for nmx,dth in angs:
of = open(name+nmx+'.inp','w')
of.write(pref % name)
cf = open('moieties/'+c)
thetlin=cf.readline()
theta = float(thetapat.match(thetlin).group(1)) + dth
for ln in cf.readlines(): of.write(ln)
for ln in open('moieties/'+l).readlines(): of.write(ln)
for ln in open('moieties/'+r).readlines(): of.write(ln)
of.write('\n')
of.write(' theta = %f\n' % theta)
of.write(' dxl = %f\n' % Rzeros[le+lb+ce])
of.write(' dxr = %f\n' % Rzeros[ce+rb+re])
of.write(' $END\n')
of.close()
|
