More options for wrapping

[hejamu]

Is your feature request related to a problem?

Most analyses become simpler when working in the "brick shape" representation of triclinic boxes. It would be nice to have the option to select the representation when wrapping (and possibly unwrapping?).

Describe the solution you'd like

Similar to gmx trjconv -ur:

u.atoms.wrap(representation="tric")  # default behaviour
u.atoms.wrap(representation="rect")  # brick shape, does nothing for orthorhombic boxes
u.atoms.wrap(representation="compact")

See #2982 for the importance of compact wrapping.

Describe alternatives you've considered

We currently do this

is_triclinic = np.any(ts.dimensions[-3:] != np.array([90.0, 90.0, 90.0]))
self._universe.atoms.wrap(compound=self.wrap_compound)
if is_triclinic:
    ortho_box = triclinic_to_orthorhombic(ts.dimensions)
    self._universe.atoms.wrap(
        compound=self.wrap_compound, box=ortho_box
     )

Additional context

maicos-devel/maicos#571

[PardhavMaradani]

For compact wrapping, linking this to the 'Additional Context' section of issue #5234 and the initial comment of PR #5235 that compares the implementation in #2982, which uses distance_array vs a slightly faster one using minimize_vectors (see code under 'Compact wrapping with distance_array' and 'Compact wrapping with minimize_vectors'). This could be useful during the implementation of this issue. Thanks