Dear Jun,
Thanks a lot for your response. I have done the same by utilizing VMD-Topotools which is one of the options as you said. Here is the problem I am facing:
I am duplicating my unit cell in three directions for SiO2 and doing the same for Si and my purpose is to put these two layers on top of each other. As this repetition number of the unit cell should be an integer number, so it is hard (kinda impossible) to achieve the same length in X or Y directions of my atomic configurations for SiO2 and Si, so I end up with two very close length of Si and SiO2 layers in x and y-directions. After proper energy and pressure minimization steps, I still have inconsistency at the ends (x and y) of the two layers defined in LAMMPS. I am planning to model tensile test utilizing Fix Deform command and I end up with cases which pulls my sample in X direction just from those small amounts of Si or O atoms close to the right and left the side of the layers in X direction which I am guessing is the result of having different lengths (even though its very small) for the two layers.
I am wondering if there is any way to kinda cut my layers in a way they have the same length so that I can use Fix Deform in LAMMPS. Or maybe any other suggestions for this problem?
Best,
Sina