Specifying positions

When we are calculating the defect energy for vacancies, what is the right way to specify the co-ordinates of the center and vacancy? Should the co-ordinates for center and vacancy must be same? How to specify it ?

The centre and vacancy don’t have to be at the same position, but if it’s the only defect then that would be the most sensible choice to get good convergence with increasing region size. As for how to specify them, I’d recommend looking at the commands in the help text, plus the example files (and if all else fails you can read the manual).