Avogadro cannot open a particular Gaussian 16 output file (.log extension). The older Avogadro program gives an error, “Reading molecular file failed”. The newer version gives a blank page when the GAMESS or NWChem readers are chose. Choosing OpenBabel gives an “error while reading file” message.
Other G16 log files are read without issue. The only difference I see is that the problematic log file is from a restart calculation (from the chk file).
If this is a known issue, hearing about a workaround would be great.
Avogadro version:1.20, 1.95.1
Operating system and version:
Program should open molecular model and display frequencies.
Steps to Reproduce
Please upload files if appropriate here (or via file-sharing service like Dropbox or Pastebin)
While Avo2 has readers for GAMESS or NWChem output files, they won’t do anything for you.
So if Open Babel doesn’t read it, there’s not much we can do until the OB reader for Gaussian has support for that.
OTOH, if you’re using Avogadro2, you can install
cclib to your Python environment and then install the
avogadro-cclib plugin from Extensions => “Download Plugins…”
If it’s installed, you can read files through
cclib updates faster than Open Babel can… and we’re working to improve the Avogadro / cclib integration further.
Thanks for both replies and thanks for the model picture (just like I pictured it).
Does the Avo2 download process put cclib in the right place? A related issue for me is upgrading python (as I am clinging to Mojave).
At the moment, Avogadro won’t install
cclib itself. You’ll need to use either
conda / mamba to do that.
It will download the “glue” between Avogadro and
cclib into the right place.
Yes, you will need a newer version of Python (3.6 or later).