I am running simulations for uniaxial tension of Aluminium. While
analysing the result with Atomeye I see atoms with different color. I
want to know what these color of particular atom mean, are they
denoting stresses on the atom or something else.
This is really an AtomEye question - I suggest you
consult its manual. If you are using the dump cfg option
in LAMMPS and have different atom types, it may
be outputting these is a way that AtomEye interprets
as different elements or with other flags. AtomEye
also has options to look at neighborhoods of atoms
and color accordingly, e.g. for defects.