Influence of folder name on xTB calculations

Nyama · October 30, 2025, 5:19pm

Thank you very much for your continued excellent work—and congratulations on the release of Avogadro 2 v1.102.1.

I have encountered an issue that may not strictly be a bug, but I would like to bring it to your attention as a precaution. When the input coordinate file (“.xyz”) is placed in a folder whose name is in Japanese characters, the calculation with xTB terminates unexpectedly. I’m not sure whether the same issue occurs with folder names in other languages. Aside from xTB calculations, I have not encountered any problems so far.

Environment Information

Avogadro version: 1.102.1
Operating system and version: windows11

ghutchis · October 30, 2025, 6:48pm

I think @matterhorn103 can comment on this. I think it’s related to this issue (still):

github.com/OpenChemistry/avogadrolibs

Plugin output to console doesn't use Unicode on Windows, Avogadro expects UTF-8

opened 07:41PM - 12 Feb 24 UTC

matterhorn103

bug good first issue plugins python

See [this issue](https://github.com/matterhorn103/avo_xtb/issues/2) on the avo_x…tb plugin repo, helpfully raised by @Ineluki80. It seems that on Windows, in at least some cases, the Python stdout stream isn't being encoded in UTF-8 but rather that of the system locale/extended ASCII, which means Unicode characters (e.g. the ellipsis for menu options) are being garbled. The Python `sys` [docs](https://docs.python.org/3/library/sys.html) suggest that actually in many cases, UTF-8 is the default, so I'm not quite sure what's going on. In any case, it looks like there are various ways to enforce Unicode when calling the interpreter e.g. via an environment variable or a command line flag.

Let’s see if we can get a fix that works for you.

matterhorn103 · October 30, 2025, 8:16pm

Yeah, I think you’re probably right as to the origin of the issue. In any case, I’d be keen to get to the bottom of it.

Edit: Having said that, I thought I’d also already fixed this by enforcing UTF-8 on the plugin side, see this old closed issue.

Thinking of possible causes, it might be that:

I have only enforced UTF-8 output using sys.stdout.reconfigure(encoding='utf-8'), and haven’t told Python to read stdin as UTF-8
Whatever is put out by the .toLocal8Bit() method that Avogadro is using isn’t then decoded by Python properly
I forgot to specify the use of UTF-8 in one of the file IO operations in avo_xtb or easyxtb somewhere
xtb doesn’t expect UTF-8 files on a non-UTF-8 machine