Writing xyz files to the same location has interesting results...

[PeaWagon]

... by interesting, I mean it doesn't write the correct output. May have to find a bug in Kaplan or Vetee.

What happened:
When the output was directed to the kaplan_output directory of the git repository, the file was overwritten (in the sense that the time stamp was changed), but the new molecule was not added to the xyz file (it was still butane and not ethanol).

What is puzzling:
This problem doesn't occur when running outside of the github repository. Perhaps that is the problem (if version control doesn't allow for the update to run).