Calculating interaction energy by using script

Hi Dear All
I tried to calculate interaction energy between a layer of clay and the solute ions. I used the script from
(Updated Link​​​​​​​)
I used the latest version of the author, but I still got the problem met by other people mentioned about, the interaction energy I calculated between four solute ions and the clay was almost four time larger than the interaction energy calculated between one solute ion and the clay. 
Could you please help me out with that? What's the problem here? Thank you very much!

Regards,
Jingjing Bu