Fix apply_operation(fractional=True)

[kavanase]

Summary

Structure.apply_operation() fails when using the fractional=True operation.
The issue is that the SymmOp is applied to the site frac coords (in the original lattice), but then these new frac coords (in the old basis) are used directly with the new (transformed) lattice, giving a 'doubled' transformation and messing with the output.

Fix added here, matching the implementation in doped (which also has a couple more options and a cleaner implementation).

MWE:

(Notebook and structure being used attached too as always 😉 , with more examples)

Pymatgen_SymmOp_Fix_PR.zip

[kavanase]

This fixed implementation is tested and shown to be working in the attached notebook as well

[janosh]

thanks a lot for the fix @kavanase. could you add a unit test that covers this change?

[kavanase]

Done!
Also checked that this test fails with the old code (for fractional=True), but works all fine with the new code.

[janosh]

thanks, good stuff!