Allow a.u. xyz import, DALTON input generator bugs and wayland support


I have a QoL suggestion for xyz import. It would be nice if other units than Angstrom were allowed to import/export from/to xyz, for example the atomic unit of length used in quantum chem.

Secondly, I would like to point out a bug in the DALTON input generation. I understand that it is probably handled by an extension I installed (Avogenerators). I don’t have a github account to open an issue, though.
I have found the following issues:

  1. the .mol and .dal files are the other way around
  2. when choosing an operation other than Single Point, it always displays an input file for an HF calculation, rather than the chosen method (e.g. DFT)
  3. when opening the input generator menu for DALTON, while there is no molecule present, error messages are displayed (presumably due to no atoms having been drawn)
  4. Submit calculation… is greyed out, with no clear indication on how to make it work

Thirdly, I would like to ask about wayland support. I am on GNOME on fedora linux. The X11 version of Avogadro works perfectly, besides minor graphical glitches (e.g. wrong menu highlighted with the blue underline) presumably due to it using xwayland. The wayland version, however cannot render anything.

Thank you for an amazing FOSS molecule editor though!!!

The .xyz format is standardized around Angstrom. It’s possible to copy coordinates in Bohr if you want, e.g. from the Coordinate editor, or you can set up an input generator for the format you want, or you can use other output formats through Open Babel or Python scripts.

Please submit a bug report to the avogenerator GitHub repo (e.g. avogenerators/ at 582879c62b78b7c8a4e34c65a6027a4efa627b2f · OpenChemistry/avogenerators · GitHub)

They’re just Python scripts. Not sure why #2 is happening, but the others can easily be fixed. We just haven’t had many Dalton users evidently.

This uses Molequeue, which at the moment has fallen by the wayside. For the moment, the next release will hide the button until Molequeue can be resurrected.

There’s an open issue: Add support for Wayland · Issue #567 · OpenChemistry/avogadrolibs · GitHub

As far as I can tell, the main thing is to drop the glew project for a better OpenGL support library.