Thanks a lot for your nice input. I will keep these things for further calculations.

I encountered numerical artifacts during optimization, for example:

Consider 2D square lattice with two atoms (A&B) basis (side of square lattice = a*sqrt(2)) where 'a' is the bond length, the atomic position in fractional coordinates A(0,0,0.5) & B(0.5,0.5,0.5). Now upon geometry optimization, the fractional coordinates remain the same but the cartesian coordinates show some non-zero values in of x and y plane for atom A, of the order of 10^-10 or even smaller time. Like atom A being at ( -10^-12, -10^9, 0.5).

Is this numerical noise could be the cause of imaginary modes?