I wonder if somebody can help me figure out a behavior I see in Avogadro related to output files from ORCA 4.2.1. I am using an Ryzen AMD processor and Windows 10, 64 bit. Avogadro 1.2.0n-win32.
When I load an *.OUT file including vibration information (Raman, IR) from ORCA into Avogadro. The molecule loads fine, and the “Vibrations” toolbar opens well showing the list of vibrations. Unfortunately, if I click the button “Start Animation”, I get the message: “No vibrational displacements exist”. If I click “Start Animation” anyway, Avogadro stops responding and has to be shutdown from the Task Manager.
I can see the animation of the vibrations if I use ORCA_PLTVIB.exe command and export each vibration into an XYZ file separately, AND THEN open that file with Avogadro. This of course is a bit of a shore for molecules with upwards of 50 vibration modes.
Is there a way to put a random vibration displacement for all frequencies? I see the option “Normalize displacements”, but it doesn’t do anything in this case.
I believe this to be a bug with Avogadro
Environment Information
Avogadro version: 1.2.0n win32
Operating system and version: Win 10 Pro 64 bit
Expected Behavior: molecule showing each vibration
Actual Behavior: message saying “no vibration displacement exist”
Steps to Reproduce: click on vibration frequency on the “Vibrations toolbar”
Please upload files if appropriate here (or via file-sharing service like Dropbox or Pastebin)
Ok, I figured out the problem. If you LOGIN to the ORCA website (https://orcaforum.kofo.mpg.de/app.php/portal) after signing in, you can download AVOGADRO WITH ORCA SUPPORT. The file is called: “AvogadroOrca4.1.exe”. After installing this version (I did NOT uninstall the previous version). Now the vibration mode works as intended. It is great. I am so happy. I hope this can help somebody else that might have missed that there was an Avogadro version specifically to be used with ORCA. By the way, the Application Version (from Help) is 1.2.0 (at least it is today July 16/2020). Keep the good work.
Carlos
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I suspect that the output format from Orca changed slightly. They do put out builds with Orca support, and certainly you can use that.
If you can post or send me an output file, I would appreciate it - to make sure we can parse newer files.
Thanks!
Yes, I figure that is what happened. I will be happy to send you an *.out file with vibrations. Actually, I will past it below as well. The input file running a sort of “Polyvinylpyrrolidone” monomer on 8 cores, solvated in water was:
B3LYP-gCP-D3/6-31G* page 420 of the manual
Using 8 cores - Run full path of ORCA d:\orca\orca PVP.inp > PVP.out
! B3LYP-gCP-D3/6-31G* TightOpt TightScf Grid6 NoFinalGrid NumFreq PAL8
%freq
CentralDiff true
Increment 0.005
end
%elprop Polar true end
%CPCM SMD TRUE
SMDSOLVENT “WATER”
END
- xyz 0 1
O -0.578757 -1.850143 0.627175
N 0.389530 0.075241 -0.195828
C -1.382054 1.604585 0.032145
C -0.012781 1.398002 -0.647844
C -1.914025 0.177539 0.217469
C -0.654613 -0.690433 0.271785
C 1.712868 -0.474197 -0.422796
C 2.786477 0.096766 0.505744
H -2.045751 2.254473 -0.557178
H -1.236164 2.082307 1.014515
H -0.094048 1.429813 -1.754324
H 0.722177 2.166199 -0.354445
H -2.515587 -0.162562 -0.644751
H -2.525848 0.025081 1.118144
H 3.763430 -0.364750 0.288815
H 2.539536 -0.106393 1.560216
H 2.901648 1.186797 0.384033
H 1.620603 -1.560896 -0.271800
H 1.995918 -0.306829 -1.479806
-
I’ll send you the out file by email. I just realized the system does not allow too many characters here.
Carlos
Hello, what version of Orca did you use when viewing the output file in AvogadroOrca4.1.exe? I currently am running avogadro 1.2.0 and downloaded this version of avogadro as well WITHOUT deleting the initial version, but to no avail. I have tried with Orca 4.2.1 which seems to be the one you used as well.
I’m not quite sure I understand your message. It sounds like you’ve run an Orca 4.2.1 calculation, and you’re using Avogadro 1.2 and cannot read a vibrational output?
I’d suggest downloading https://two.avogadro.cc/ including a nightly.