Thanks for the reply Andrew.
The problem is geometrical, as u said. What we do in MATLAB is define the mag. as well as direction for the coordinates generation.
The vacuum gap in the image posted earlier is overcome( As Said by Axel) by giving the direction as the conventional ones i.e 1 0 0 , 0 1 0 and 0 0 1 and incorporating the orientation into the “magnitude” when we define the atom coordinates. Then the whole box is filled with atoms in the LAMMPS post-processing softwares , like ATOMEYE, and the problem just works fine.