Reducing unit cell to primitive transforms instead of removes redundant atoms.

[brockdyer03]

Avogadro version:

• Avogadrolibs: 1.103.0
• Qt: 6.8.3

Desktop version: (please complete the following information):

• OS: Fedora Linux
• Version: 43

Describe the bug
Reducing a unit cell to its primitive form should remove any atoms that are not either inside of or the boundary of the new primitive cell, however currently atoms are wrapped into the primitive cell.

To Reproduce
Steps to reproduce the behavior:

1. Import any crystal or CIF file, I recommend halite.
2. Select Reduce to Primitive in the "Crystal>Space Group" menu
3. Use default tolerance
4. See error

Expected behavior
I expect the unit cell to go from this:

to this:

[ghutchis]

Yeah, basically 'reduce to primitive' should go back to the asymmetric unit, generate the primitive, then fill any symmetric sites.

And I'll need to think how to add some unit tests for this.

[brockdyer03]

I was checking out the C++ code for this, and it seems like the actual determination of the primitive cell is handled by spglib. I think it'd be relatively trivial to implement on the Avogadro side, but perhaps there is some part of the spglib C API that does that automatically?