Support `FixAtoms` constraints with the `Vibrations` class

Closes #1479 (closed).

Previously, the Vibrations module did not respect the FixAtoms constraint of the Atoms underlying object, which is somewhat counterintuitive. In this MR, we adjust indices (only if indices is not specified by the user!) to reflect the unfixed atoms in the Atoms object.

Checklist

• I am familiar with ASE's contribution guidelines.
• Doc strings in code changed in this MR are up to date.
• Unit tests have been added for new or changed code.
• Issue is resolved via "closes #XXXX" if applicable.