Hi Lammps users
I have a dump file with positions, mass, type, box image of the atoms. But I forgot to dump the atom ID. I have finished a largar number of simualtions. So it is time consuming to redo them. So,instead of redoing them, I wander if there is a tool or command in lammps which can restore the atom ID and sort it, then output the dump file again with ID?
You forgot the atom ID? If so, how would a tool even be able to restore the atom ID?
You would need to write a tool yourself using some heuristic to follow the identity of atoms.
A simple approach would be to make an initial atom ID assignment and then compare frames (after unwrapping coordinates). Atoms with the same ID should have the shortest displacement between two frames assuming individual frames are stored sufficiently frequent.