(De)Protonate leads to deleted .CHRG file

[hoelzerC]

Describe the bug
The .CHRG files is deleted during (de)protonation.

To Reproduce
Create a folder with struc.xyz and .CHRG (arbitrary charge) and run crest struc.xyz --protonate or crest struc.xyz --deprotonate.

Expected behavior
Leave existing files intact, i.e. not delete the .CHRG file.

[hoelzerC]

Add: When charge != 0 the file is not deleted, but altered. Wondering why crest is modifying these files at all.

[pprcht]

We have used it in the past to track the charge of the protonated structure, which is the modified file you mention. It is user-responsibility to provide the correct input charge, and this should be done via the cli (-chrg), not hidden files.

That said, I won't modify the legacy code since it has done this thing for four years now and it's not a bug. Furthermore the new (calculator rather than xtb-based) implementation is already written. It is not yet the default, but can be selected with --newversion