determination of structure after NPT run

Dear LAMMPS users,
how can one verify after a NPT run that quartz remained as quartz (quartz is a generic here). Maybe this is same as asking how one can determine the crystal structure from a given set of atomic coordinates. A snapshot from a MD dynamics will record the displacements due to thermal vibrations, how that will be taken care of while determining the structure? I know this is not exactly a lammps question, but I couldn’t find the answer elsewhere. My apology for that.

There are several computes which look at the local

neighbors of each atom and calculate quantities

related to crystal structure. E.g. compute coord/atom,

compute centro/atom, compute cna/atom.


...or use one of those RMSD fit and alignment tools that people in
biosimulations use to determine how much (and where) their protein
structure has changed.