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
|
#! /usr/bin/env python
ATOMIC_NUMBERS={
"H": 1,
"He": 2,
"Li": 3,
"Be": 4,
"B": 5,
"C": 6,
"N": 7,
"O": 8,
"F": 9,
"Ne": 10,
"Na": 11,
"Mg": 12,
"Al": 13,
"Si": 14,
"P": 15,
"S": 16,
"Cl": 17,
"Ar": 18,
"K": 19,
"Ca": 20,
"Sc": 21,
"Ti": 22,
"V": 23,
"Cr": 24,
"Mn": 25,
"Fe": 26,
"Co": 27,
"Ni": 28,
"Cu": 29,
"Zn": 30,
"Ga": 31,
"Ge": 32,
"As": 33,
"Se": 34,
"Br": 35,
"Kr": 36,
"Rb": 37,
"Sr": 38,
"Y": 39,
"Zr": 40,
"Nb": 41,
"Mo": 42,
"Tc": 43,
"Ru": 44,
"Rh": 45,
"Pd": 46,
"Ag": 47,
"Cd": 48,
"In": 49,
"Sn": 50,
"Sb": 51,
"Te": 52,
"I": 53,
"Xe": 54,
"Cs": 55,
"Ba": 56,
"La": 57,
"Hf": 72,
"Ta": 73,
"W": 74,
"Re": 75,
"Os": 76,
"Ir": 77,
"Pt": 78,
"Au": 79,
"Hg": 80,
"Tl": 81,
"Pb": 82,
"Bi": 83,
"Po": 84,
"At": 85,
"Rn": 86,
"Fr": 87,
"Ra": 88,
"Ac": 89,
"Ku": 104,
"Ha": 105
}
class Parser:
def __init__(self,infile_name):
self.infile_name=infile_name
try:
i=open(self.infile_name,'r')
except IOError:
print "No such file or directory:",self.infile_name
import sys
sys.exit()
input=i.readlines()
i.close()
self.molecules=self._parse(input)
def _parse(self,input):
molecules={}
count=0
for line in input:
if line[0] == '#':
if count > 0:
molecules[name]=data
name=line[1:].split()[0]
if name in molecules.keys():
print name,"used more than once"
import sys
sys.exit(1)
data=[]
count+=1
else:
l=line.split()
a=l[3]
atom=a[0].upper()+a[1:]
d=[atom,float(l[0]),float(l[1]),float(l[2])]
data.append(d)
if count > 0:
molecules[name]=data
return molecules
def Molecules(self):
return self.molecules.keys()
def NumberOfMolecules(self):
return len(self.Molecules())
def Atoms(self,molecule):
return [x[0] for x in self.molecules[molecule]]
def toXYZ(self,molecule,comment="",conversion_factor=0.52917720859):
c=conversion_factor
s=""
if molecule in self.Molecules():
atoms=self.molecules[molecule]
s+=str(len(atoms))+"\n"
s+=molecule+" "+comment+"\n"
for atom in atoms:
s+="%-6s %20.14f %20.14f %20.14f \n" %(atom[0],c*atom[1],c*atom[2],c*atom[3])
return s
def AlltoXYZ(self,comment=""):
s=""
for molecule in self.Molecules():
s+=self.toXYZ(molecule,comment=comment)
return s
def toSewardInput(self,molecule,basis="$Basis.....",unit="/Angstrom",conversion_factor=0.52917720859):
c=conversion_factor
s=""
if molecule in self.Molecules():
s+=" &SEWARD &END\n"
s+="\nTitle\n"
s+=" "+molecule+"\n\n"
labels={}
atoms=self.molecules[molecule]
for atom in atoms:
if atom[0] in labels.keys():
labels[atom[0]]+=1
else:
labels[atom[0]]=1
mylabel=atom[0]+"_"+str(labels[atom[0]])
s+="\nBasis Set \n"
s+=atom[0]+"."+basis+"\n"
s+="%-6s %20.14f %20.14f %20.14f %-10s \n" %(mylabel,c*atom[1],c*atom[2],c*atom[3],unit)
s+="End Of Basis\n"
s+="\nEnd Of Input"
return s
def toBlockedSewardInput(self,molecule,basis="$Basis",unit="/Angstrom",conversion_factor=0.52917720859):
c=conversion_factor
s=""
if molecule in self.Molecules():
s+=" &SEWARD &END\n"
s+="\nTitle\n"
s+=" "+molecule+"\n\n"
labels={}
atoms=self.molecules[molecule]
for atom in atoms:
if atom[0] in labels.keys():
labels[atom[0]]+=1
else:
labels[atom[0]]=1
for label in labels.keys():
s+="\nBasis Set\n"
s+=label+"."+basis+"\n"
i=0
for atom in atoms:
if atom[0] == label:
i+=1
if labels[label] == 1:
mylabel=atom[0]
else:
mylabel=atom[0]+"_"+str(i)
s+="%-6s %20.14f %20.14f %20.14f %-10s \n" %(mylabel,c*atom[1],c*atom[2],c*atom[3],unit)
s+="End Of Basis\n"
s+="\nEnd Of Input"
return s
def SCFInput(*args):
s="\n &SCF &END\n"
for arg in args:
s+=str(arg)+"\n"
s+="End Of Input"
return s
def addKeywordsToInput(input,*args):
s=""
for line in input.split("\n"):
if line == "End Of Input":
for arg in args:
s+=str(arg)+"\n"
s+="\n"
s+=line+"\n"
return s
if __name__=="__main__":
import sys
inp=sys.argv[1:]
if len(inp)==0:
print "No input file specified"
sys.exit()
# parse input file
data=Parser(inp[0])
# get list of molecules
molecules=data.Molecules()
# sort the list alphabetically (in place)
molecules.sort()
# for each molecule:
for molecule in molecules:
# get a seward input file (a string), assuming bohr as unit in input file
input=data.toBlockedSewardInput(molecule,basis="$Basis",unit="/bohr",conversion_factor=1.0e0)
# add CD keywords to seward input
input=addKeywordsToInput(input,"$Seward_Options")
# Count number of electrons in neutral system
Ne=0
for atom in data.Atoms(molecule):
Ne+=ATOMIC_NUMBERS[atom]
# add an SCF input section (set charge if needed)
if molecule[-1] == "-":
# add 1 to number of electrons
Ne+=1
# UHF for odd number of electrons, else RHF
if Ne%2==1:
model="UHF"
input+=SCFInput("UHF","Charge"," -1","$SCF_Options")
else:
model="RHF"
input+=SCFInput("Charge"," -1","$SCF_Options")
else:
# UHF for odd number of electrons, else RHF
if Ne%2==1:
model="UHF"
input+=SCFInput("UHF","$SCF_Options")
else:
model="RHF"
input+=SCFInput("$SCF_Options")
# write input to file molecule.inp
file="input/"+molecule+".input"
f=open(file,"w")
print >>f, input
print molecule,"\t",file,"\t",model
f.close()
|
