Issues viewing IR Spectra

General Discussion Support
1

Hi,

Using Avogadro on a MacBook running macOS Monterey. Have used ORCA to run calculations and upon importing the .out file into Avogadro to view IR spectra, I’m not getting the expected IR data, and am instead getting a straight line. Is there a fix to this? (The spectra comes up fine on windows based users).
Many Thanks :slight_smile:

2

First off, what version of Avogadro are you using?

More important, can you post the .out file somewhere?

3

It’s the 1.2.0 version (Git Revision c1fcc5b)

INPUT FILE

NAME = aBenFreq.inp
| 1> # avogadro generated ORCA input file
| 2> # Basic Mode
| 3> #
| 4> ! B3LYP FREQ def2-TZVP NormalPrint NormalSCF
| 5>
| 6> * xyz 0 1
| 7> C -1.98696220332013 3.85682048351227 -0.00000000935197
| 8> C -3.13905173138372 3.07662103273749 -0.00000000469145
| 9> C -3.03940062616741 1.68881490965903 -0.00000001854970
| 10> C -1.78757037410137 1.08129032173894 -0.00000006442203
| 11> C -0.63548091526962 1.86148871774582 -0.00000006058181
| 12> C -0.73513364654092 3.24929554745366 0.00000006300107
| 13> H -4.11339585362064 3.54970692263513 -0.00000003891324
| 14> H -3.93624798290731 1.08152399711262 -0.00000004837298
| 15> H 0.16171467394192 3.85658549606124 -0.00000009602599
| 16> H -2.06460720652650 4.93716573726600 0.00000012721235
| 17> H -1.70992668358178 0.00094490193454 0.00000015635101
| 18> H 0.33886254947747 1.38840193214326 -0.00000000565526
| 19> *
| 20>
| 21>
| 22> END OF INPUT

IR SPECTRUM

Mode freq eps Int T2 TX TY TZ
cm-1 L/(mol*cm) km/mol a.u.

6: 412.35 0.000000 0.00 0.000000 ( 0.000006 -0.000004 -0.000106)
7: 412.69 0.000000 0.00 0.000000 (-0.000003 -0.000006 -0.000106)
8: 623.62 0.000000 0.00 0.000000 (-0.000000 0.000000 -0.000000)
9: 623.70 0.000000 0.00 0.000000 ( 0.000000 -0.000000 -0.000000)
10: 687.35 0.022296 112.68 0.010123 (-0.000003 -0.000001 0.100611)
11: 714.62 0.000000 0.00 0.000000 ( 0.000002 -0.000001 0.000000)
12: 861.93 0.000000 0.00 0.000000 ( 0.000001 0.000001 0.000001)
13: 861.95 0.000000 0.00 0.000000 (-0.000000 -0.000001 -0.000000)
14: 962.75 0.000000 0.00 0.000000 ( 0.000002 0.000003 0.000031)
15: 962.78 0.000000 0.00 0.000000 ( 0.000002 -0.000000 -0.000057)
16: 990.78 0.000000 0.00 0.000000 ( 0.000001 0.000000 -0.000001)
17: 1014.08 0.000000 0.00 0.000000 (-0.000000 -0.000000 -0.000000)
18: 1029.74 0.000000 0.00 0.000000 (-0.000183 -0.000303 -0.000000)
19: 1060.13 0.001077 5.45 0.000317 ( 0.012166 0.013006 -0.000000)
20: 1060.39 0.001009 5.10 0.000297 (-0.013083 0.011211 0.000000)
21: 1176.40 0.000001 0.00 0.000000 (-0.000371 0.000275 -0.000000)
22: 1198.91 0.000000 0.00 0.000000 (-0.000000 -0.000000 -0.000000)
23: 1199.11 0.000000 0.00 0.000000 ( 0.000000 0.000000 0.000000)
24: 1334.07 0.000000 0.00 0.000000 (-0.000038 0.000109 0.000000)
25: 1388.01 0.000000 0.00 0.000000 ( 0.000000 -0.000000 -0.000000)
26: 1516.64 0.001476 7.46 0.000304 (-0.001894 -0.017326 -0.000000)
27: 1516.78 0.001507 7.62 0.000310 (-0.017521 0.001747 -0.000000)
28: 1634.84 0.000000 0.00 0.000000 ( 0.000000 0.000000 0.000000)
29: 1634.98 0.000000 0.00 0.000000 ( 0.000000 0.000000 0.000000)
30: 3157.94 0.000004 0.02 0.000000 ( 0.000466 0.000444 -0.000000)
31: 3167.19 0.000000 0.00 0.000000 (-0.000002 -0.000001 -0.000000)
32: 3167.37 0.000000 0.00 0.000000 (-0.000001 0.000001 -0.000000)
33: 3182.25 0.007580 38.31 0.000743 (-0.024116 -0.012718 0.000000)
34: 3182.57 0.007114 35.95 0.000698 (-0.012273 0.023387 0.000000)
35: 3192.46 0.000000 0.00 0.000000 ( 0.000000 0.000001 -0.000000)

Theres my .inp lines and the IR data from the .out

4

I actually need the full output file. Could you ZIP it or put it on Google Drive or Dropbox?

If not, try Pastebin or Gist.GitHub.com so I can try the whole file.

(And is this Orca4 or Orca5?)

5

Orca 5
aBenFreq.out , and a link to the output file in onedrive :slight_smile:

6

Yeah, it seems as if Orca 5 changed the format of the IR spectra somewhat, breaking the parser. :frowning:

I can update Open Babel, but it won’t help Avogadro 1.x.

At the moment, the holdup is that Avo2 doesn’t have a spectra plot either, but hopefully soon.

Workarounds:

  • I’m not sure if the orca_2mkl tool writes vibrations, but that could work.
  • orca_mapspc will generate the text files with the broadening for plotting in your favorite program.

I’d go with orca_mapspc which works well from the command-line.

7

Amazing, thank you so much!