I am trying to setup Avogadro 2 on Windows 11 to view the outputs of gaussian09 scans and irc calculations. I would like to open the gaussian .log file in Avogadro and view the energy vs scan step graph and be able to view the geometry at each scan point.
Is this possible? How can I do this?
I can’t say if the reference files about Gaussian for the Jmol project include one to monitor a reaction performed in silico. However, given Avogadro likes the input understood by OpenBabel and
obabel -L formats
g09 -- Gaussian Output [Read-only], a first step likely should be to substitute the file extension , i.e. to rename file
example.log as file
example.g09. Does this render your output file amenable to Avogadro?
If you’re using a recent build (e.g., a nightly) you should get the scan steps (e.g., using the animation tool) when you read the file in.
At the moment “graph” is the problem - we had used VTK for graphing and that’s broken. I’ll be switching plots to use a new library, but it’ll be a bit before I have time for that.
Thank you for the replies.
OpenBabel works well to convert between chemical format files and the output is readable by Avogadro. The issue is that if the scan fails before it has completed, then OpenBabel saves every structure from optimisation steps at each scan point. Not just the minimum energy structure for each scan point. I don’t know if there is any code that extracts the minimum energy structure for each scan point?
Yes I am using the most recent build and Avogadro can read in the scan steps using the animation tool. Again, the issue comes when the scan fails, or ‘normal termination of Guassian’ is not achieved, then all geometries are included in the animation, not just the minimum energy structure at each scan point.
In terms of plotting energies along side the structures in Avogadro, this would be a very useful feature of Avogadro for all calculation types, not just the scans.
Do the logs include a unique label (e.g., i = 3 for three scan points, and j = 4 for four geometries each) to recognize e.g., 2.4 is about the fourth geometry of the second scan point? If so perhaps this could serve as a reference point to read out the geometry and the corresponding energy (assuming there is a distinct keyword in the same block/sub section). Later, the script would report only the structure(s) of lowest energy per checkpoint (e.g., 1.2, 2.4, 3.1).
Though not applicable 1:1 here (because openbabel might not equally access the energy Gaussian reports), this line of thought is based on the observation that openbabel allows to annotate e.g., .xyz files with properties as a comment after the mandatory statement of the number of atoms. E.g. about methanol (molecular weight about 32 g/mol):
$ obabel -:"CO" --gen3d -oxyz --append "MW"
C 1.09976 -0.01803 -0.03464
O 2.51549 -0.02861 -0.03300
H 0.73825 0.34952 -0.99815
H 0.73825 0.62484 0.77168
H 0.73668 -1.03628 0.12376
H 2.80840 0.88751 -0.17551
1 molecule converted
Thus the guess that it could be possible to report for each screening point both structure and energy about the structure of lowest energy in one file.
1 molecule converted above of course only is a comment obabel completed the work. It does not belong to the .xyz file written when calling
$ obabel -:"CO" --gen3d -O methanol.xyz --append "MW"
Yes, I think
cclib can do that: https://cclib.github.io/
I take your point about the Open Babel import - that would be a good feature to add.
Yes, no kidding. Unfortunately, during the semester, I’m teaching and doing research as well as trying to keep things moving with Avogadro. As a result, development slows down. I’m happy to collaborate, bring new contributors on board, as well as working to get funding for full-time developers.