Hi Arnau_
I am very interested in the idea you mentioned, which is necessary to calculate the angular velocity and angular momentum of a rotating non-rigid body. For non-rigid systems, atoms can vibrate or even rotate around their own equilibrium positions, and the whole non-rigid body can rotate as well. In the case where these motions exist at the same time, the angular velocity calculated by LAMMPS (variable omega() function or compute omega/chunk) does not seem to be the true angular velocity of the overall rotation of the non-rigid body, because it also includes the contribution of the local vibration or rotation of the atoms. I also asked a similar question in the lammps community, which relates to your comment about decoupling local motion from overall rotation. Questions about compute omega - LAMMPS / LAMMPS Beginners - Materials Science Community Discourse (matsci.org)
I wonder what your progress is now, can the current version of LAMMPS calculate the angular velocity of non-rigid body rotation? If it is convenient, can you provide me some help, thank you very much!