Added logger to surface warning messages.

[ojeda-e]

Fixes #79

Changes include:

• [x] Added logger to warning messages in surface.py when atoms fall outside boundaries.
• [x] Updated message to provide more informations.
• [x] Added tests to raise warning messages using negative coordinates.
• [x] Added tests to raise warning messages using (too large) positive coordinates.

Thanks @orbeckst for pointing this out in previous reviews. Tagging also @lilyminium in case she's available to check this PR.

To start, will assign @hmacdope as a reviewer.

Thanks!

[codecov[bot]]

Codecov Report

Merging #83 (b329b4f) into main (f2c4e19) will not change coverage. The diff coverage is 100.00%.