a) create_box 2 nameYourBoxHere
b) create_atoms 2 box
c) pair_coeff * * /pathToPotentialsDirectory/Cu_mishin1.eam.alloy Cu Cu (in this case a copper potential)
d) Define your groups. You may use “compute cna/atom” or “compute centro/atom” commands to do this, with appropriate parameters.
e) set group nameOfGroup1 type 1
set group nameOfGroup2 type 2
I used paradigm like this when I wanted to track the atoms as if they were divided into two groups from the beginning. But you want to divide the atoms into two groups each time you output data (write to the dump files). In this case I wouldn’t use type 1 type2, but rather play with the above computes (centro/atom is quicker) and per atom variables, and then include in the dump files the per-atom quantity, such that it will be a binary array. From here it’s straightforward to visualize with OVITO.
Good luck
Eyal Oren