use logging in output.py

[codecov[bot]]

Codecov Report

Attention: Patch coverage is 89.47368% with 2 lines in your changes missing coverage. Please review.

Project coverage is 43.56%. Comparing base (f76e26c) to head (221ecdc). Report is 19 commits behind head on main.

Files	Patch %	Lines
cp2kdata/output.py	85.71%	2 Missing :warning:

Additional details and impacted files

```diff @@ Coverage Diff @@ ## main #64 +/- ## ======================================= Coverage 43.56% 43.56% ======================================= Files 32 32 Lines 1988 1988 ======================================= Hits 866 866 Misses 1122 1122 ```

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