Hello guys.
I have tried to make a python file that can import xyz coordinates from output file after geometry optimization and create a new input file automatically to do other jobs (like sp calculation) using the optimized coordinates.
So I wrote codes and got a new input file, but there was a problem.
When I submitted it to Qchem program and the calculation was proceeded, there was a change in coordinates represented by ‘Standard Nuclear Orientation’. You can check it below.
I think the input file is ok as the coordinates don’t need to be arranged clearly if there is a blank between the coordinates.
But I have never seen this situation when I made a new input file from the optimized output file by handmade.
So I wonder whether it is ok to continue the calculation.
A new input file by a python programming
$molecule
0 1
N 6.0382993654 3.8132988997 -0.4555276482
C 4.9864438977 4.2990168568 -1.2164856476
C 3.9135235709 3.3203534079 -1.5135810805
C 6.2027919159 2.5279327012 0.0497140536
C 5.1058348486 1.5837543099 -0.2617172763
C 3.9948849765 1.9890998611 -1.0403906428
C 2.8320071623 3.7259003188 -2.2592401065
C 1.7886156335 2.8356409139 -2.516702544
C 1.8084135217 1.5375556778 -2.0293002957
C 2.9453649299 1.0716740171 -1.3135139273
C 5.1566983114 0.3067862381 0.2296411736
C 4.147074806 -0.6152445182 -0.0738308777
C 3.0423250546 -0.280151331 -0.8416821219
C 0.6727859737 0.6324026277 -2.217618243
C 1.9839069919 -1.2445207727 -1.2165475546
C 0.8211365828 -0.7516093271 -1.9044779455
C -0.5480608552 1.1057017094 -2.6701516749
C -1.6273484195 0.2504507052 -2.8872355459
C -0.256459703 -1.6222624821 -2.2082540885
C 1.9911248557 -2.6026791737 -0.90334138
C 0.9917942632 -3.4849244248 -1.3465030731
C -0.1292851681 -3.0112818308 -1.963350785
C -1.4814419795 -1.0986847745 -2.6820298962
C -2.6534304523 -1.9796217269 -2.8708260323
C -1.2568990353 -3.9339521378 -2.2299970739
N -2.4003588258 -3.3366134103 -2.7389833066
O 7.187457522 2.2366236716 0.6960901489
O 4.967767673 5.45368651 -1.5946968519
O -3.7720239694 -1.5729018426 -3.1167881429
O -1.2302107648 -5.1278477665 -2.0019698761
H 6.7815402338 4.4712601056 -0.2487632572
H 2.8072494334 4.7450428287 -2.6294787263
H 0.953608376 3.1836858311 -3.1091982696
H 5.9916045077 0.0173947697 0.8566145453
H 4.26728753 -1.611330997 0.3003439625
H -0.6987969327 2.164458991 -2.8268313571
H -2.5891984214 0.6291628631 -3.2093196846
H 1.0725828682 -4.5372402981 -1.1030151135
H -3.2132860161 -3.9363849536 -2.8190094683
O 2.9967859427 -3.1774228083 -0.1681547536
C 2.9372683697 -3.3648715769 1.2052601635
C 1.7907175585 -3.387381658 2.0124859029
C 4.1972117012 -3.5869911348 1.7617058802
C 1.9717044361 -3.6599645886 3.3749736509
C 3.2219346991 -3.8639567303 3.9364124897
C 4.346004339 -3.8255437963 3.1178826261
C 0.3895750229 -3.2152747694 1.5486932098
C -0.0975345503 -2.0018920797 1.0738562331
C -1.3965979842 -1.8952418142 0.6110191647
C -2.2815189885 -2.9712117596 0.6801562868
C -1.8028690037 -4.1755254266 1.2045059532
C -0.4855694029 -4.2998545915 1.6181275927
C -3.6856465848 -2.8876285565 0.2143649572
C -4.5110379454 -1.7725490266 0.407255902
C -5.8577209627 -1.7964586336 0.0661303734
C -6.400163198 -2.9129573339 -0.5527366147
C -5.5931029578 -4.0187472822 -0.7995955872
C -4.2641490095 -4.0043307753 -0.4046360805
H 5.0550568958 -3.5746533822 1.0975939804
H 1.0912466373 -3.6731930294 4.0071955709
H 3.3111621181 -4.0537454577 5.0011552236
H 5.3378681956 -3.984363941 3.528232073
H 0.5612381779 -1.1470785777 1.0125940681
H -1.7072505198 -0.9747473842 0.1463195757
H -2.4702067514 -5.0263979567 1.2858619407
H -0.123383932 -5.2498207328 1.9976248857
H -6.4700367876 -0.9313139214 0.2942544295
H -7.4468788649 -2.9172171802 -0.8371103543
H -6.0020525415 -4.8965600288 -1.2893789694
H -3.630734832 -4.8647852684 -0.5999721526
O -4.0060384309 -0.6515767656 1.0590036336
C -3.6756609604 0.4735514263 0.3516170311
C -2.5721098742 1.2233764147 0.7686032844
C -2.1567711881 2.3126692428 -0.0601552945
C -2.9726828614 2.7442412178 -1.1322928478
C -4.1284224047 1.9990542601 -1.4567505869
C -4.4361581255 0.8590041469 -0.7668496144
C -0.8817533227 2.9307454454 0.1109732704
C -0.558783657 4.0421946755 -0.6509298166
C -1.4166382679 4.5203097381 -1.6466942465
C -2.5925085829 3.8590501353 -1.9145855114
C -3.4352541736 4.3016834153 -3.0491560755
C -4.9963578036 2.4061340635 -2.5879080089
N -4.561764824 3.5244159522 -3.2896046009
C 0.0862196254 2.3003508685 1.0137024773
C -0.376377243 1.3048611061 1.9201057215
C -1.7350140657 0.8655530115 1.9244483001
C 1.4359670655 2.606124878 0.9751073821
C 2.3546851753 1.932718687 1.7860158936
C 1.9244045755 0.9897659275 2.6865885468
C 0.544781345 0.7049851198 2.812812949
C 0.0842354483 -0.2122601514 3.7861639736
C -1.25891923 -0.4763374659 3.8920462814
C -2.1631560113 0.0485179955 2.9593819057
C 2.9180279833 0.2193167106 3.46630488
C 1.0465523923 -0.9155681371 4.6608810778
N 2.3845223793 -0.6374805482 4.4182023313
O 4.1194220408 0.2972392573 3.2972314514
O 0.7252771632 -1.719289917 5.5159059343
O -3.179844293 5.2621980191 -3.7468752787
O -6.0152541218 1.8278608728 -2.9021629924
H -5.2757379615 0.2684747299 -1.1048659625
H 0.3879169386 4.5442279444 -0.4991948076
H -1.1542115704 5.383479677 -2.2486428283
H -5.1474486 3.8182642589 -4.0635256955
H 1.8151830895 3.3276087566 0.2638920674
H 3.4173518668 2.1215947442 1.6995979955
H -1.5965022542 -1.1540884994 4.6681488921
H -3.1989463728 -0.2459296266 3.0166902439
H 3.0522536717 -1.2148673956 4.9165386129
$end
$rem
BASIS = 6-31G*
JOB_TYPE = Optimization
exchange = CAMB3LYP
DFT_D = EMPIRICAL_GRIMME
SCF_CONVERGENCE = 8
scf_algorithm rca_diis
SCF_MAX_cycles 512
MEM_TOTAL = 8000
GUI = 0
GEOM_OPT_MAX_CYCLES = 500
XC_GRID = 75000302
THRESH = 14
$end
$empirical_dispersion
S6 1.0
$end
Standard Nuclear Orientation from a new calculation
----------------------------------------------------------------
Standard Nuclear Orientation (Angstroms)
I Atom X Y Z
----------------------------------------------------------------
1 N 6.2330866618 3.5428516533 -0.5226915966
2 C 5.1079073060 4.3448621955 -0.6328253476
3 C 3.8540971913 3.6344975881 -0.9800258529
4 C 6.3201953323 2.1666051493 -0.7039397154
5 C 5.0451707248 1.4938942940 -1.0409107393
6 C 3.8463988049 2.2339323956 -1.1828133053
7 C 2.6920841508 4.3589102690 -1.1029298133
8 C 1.4907940813 3.7080735005 -1.3872329381
9 C 1.4335099651 2.3315155548 -1.5446652743
10 C 2.6308522448 1.5663554748 -1.4902973716
11 C 5.0218227922 0.1336487998 -1.1953605500
12 C 3.8354917243 -0.5247452991 -1.5427960575
13 C 2.6343895414 0.1478821688 -1.7079651408
14 C 0.1603770115 1.6372726750 -1.7485645811
15 C 1.3760877798 -0.5141589590 -2.1192552210
16 C 0.1658052745 0.2625892744 -2.1303628552
17 C -1.0460688431 2.2889950531 -1.5510504061
18 C -2.2653193920 1.6512270880 -1.7749286215
19 C -1.0771705690 -0.3488251451 -2.4348527182
20 C 1.2513310269 -1.8632877939 -2.4464120440
21 C 0.0441681300 -2.4220743644 -2.8979936110
22 C -1.1107086856 -1.6960311299 -2.8700962947
23 C -2.2852272857 0.3573706864 -2.2322073968
24 C -3.5892605332 -0.3144928519 -2.4148205151
25 C -2.3996755393 -2.3697784354 -3.1503868413
26 N -3.5278262352 -1.5834490459 -2.9705454345
27 O 7.3818595081 1.5911748036 -0.5857091857
28 O 5.1724694381 5.5437925666 -0.4456029645
29 O -4.6543500376 0.1808495653 -2.1027466169
30 O -2.5024833261 -3.5342730246 -3.4842705780
31 H 7.0987334806 4.0167760333 -0.2900486996
32 H 2.7315747012 5.4340963850 -0.9659759937
33 H 0.5947147989 4.3061056839 -1.4811637460
34 H 5.9361724706 -0.4282967149 -1.0467224270
35 H 3.8915025080 -1.5831039681 -1.6957205594
36 H -1.0637691351 3.3030405810 -1.1773724215
37 H -3.2058042066 2.1539407659 -1.5876219515
38 H 0.0192664991 -3.4691864397 -3.1738886867
39 H -4.4171094035 -2.0630016030 -3.0491933781
40 O 2.3116976022 -2.7314659755 -2.3825903078
41 C 2.5883273260 -3.5309392106 -1.2829237860
42 C 1.7071320012 -3.9021477761 -0.2570593401
43 C 3.8990710560 -4.0086662209 -1.2953298363
44 C 2.1962693395 -4.7765975869 0.7224878818
45 C 3.5019517717 -5.2403736860 0.7251693604
46 C 4.3612806425 -4.8494185033 -0.2964505216
47 C 0.2786261441 -3.5089038479 -0.1445645525
48 C -0.1187710767 -2.2044512857 0.1302488467
49 C -1.4602312186 -1.8716150789 0.1837557001
50 C -2.4537692199 -2.8409697723 0.0466055367
51 C -2.0499087007 -4.1600909308 -0.1797478139
52 C -0.7068902108 -4.4862147549 -0.2882071485
53 C -3.8996158154 -2.5252432641 0.1198613588
54 C -4.4579845429 -1.6100063950 1.0212192292
55 C -5.8332053946 -1.4482627966 1.1356747312
56 C -6.6890485613 -2.1422221511 0.2932008955
57 C -6.1609129579 -3.0239484362 -0.6441829832
58 C -4.7898365954 -3.2186415734 -0.7117376629
59 H 4.5417765214 -3.7071408467 -2.1157610320
60 H 1.5234830604 -5.0637566775 1.5224777334
61 H 3.8381893008 -5.9021499587 1.5167847163
62 H 5.3883492819 -5.1984819873 -0.3227014473
63 H 0.6267676301 -1.4305786480 0.2474404030
64 H -1.7332865117 -0.8348840746 0.2856886843
65 H -2.7976660675 -4.9395888644 -0.2755831975
66 H -0.4119646187 -5.5106956913 -0.4909135533
67 H -6.2189810656 -0.7749410528 1.8928151332
68 H -7.7607655318 -1.9949212391 0.3721023147
69 H -6.8179653524 -3.5683964695 -1.3146613434
70 H -4.3745839095 -3.9033466815 -1.4455603648
71 O -3.6283739436 -0.9265620967 1.9049774370
72 C -3.3233271723 0.3916401351 1.6934405137
73 C -2.0448184152 0.8431315722 2.0333094425
74 C -1.6966556272 2.1840177328 1.6773419594
75 C -2.6880998677 3.0773019360 1.2077391361
76 C -3.9910868351 2.5881679819 0.9642576050
77 C -4.2815655667 1.2643838681 1.1475513940
78 C -0.3407507519 2.6290129748 1.6991350448
79 C -0.0593141717 3.9604063022 1.4377725204
80 C -1.0631422084 4.8604756299 1.0659394606
81 C -2.3570914703 4.4200142334 0.9130013825
82 C -3.3888156993 5.3524502714 0.4035871438
83 C -5.0514883467 3.4879757963 0.4500227678
84 N -4.6468613321 4.7955149243 0.2083164264
85 C 0.7192363407 1.6348099329 1.8922066555
86 C 0.3614278966 0.3421287118 2.3691877333
87 C -0.9994628799 -0.0238209335 2.5993216673
88 C 2.0415429725 1.8983392513 1.5777818662
89 C 3.0236184773 0.9093364880 1.6895526790
90 C 2.7033099056 -0.3346743527 2.1744978840
91 C 1.3790419848 -0.6195010954 2.5814145427
92 C 1.0532221204 -1.8737620866 3.1484457670
93 C -0.2384535769 -2.1315216780 3.5359328857
94 C -1.2623646910 -1.2182777937 3.2520810087
95 C 3.7330973729 -1.3967323976 2.1946848611
96 C 2.0889185224 -2.9195744946 3.2878566924
97 N 3.3417319773 -2.5861077867 2.7922280319
98 O 4.8438153731 -1.2721828142 1.7163561517
99 O 1.8822677134 -4.0211405570 3.7612504301
100 O -3.1785265683 6.5216317502 0.1517384814
101 O -6.1952324582 3.1395581337 0.2456693367
102 H -5.2629080709 0.9126941239 0.8626732478
103 H 0.9607679247 4.3176478382 1.4935751675
104 H -0.8362397823 5.8989698912 0.8507252226
105 H -5.3622031159 5.4245904873 -0.1393561809
106 H 2.3283355059 2.8594649441 1.1726171476
107 H 4.0416917721 1.0967081991 1.3720289420
108 H -0.4615882050 -3.0846239780 4.0022492670
109 H -2.2792199229 -1.4863241190 3.4908317691
110 H 4.0175783311 -3.3408603659 2.7581699923
----------------------------------------------------------------
