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Hello,
When working with supercells to model surfaces with adsorbates attached to one side only, the positions of the atoms in the bottom layers are often fixed with Selective Dynamics. Should these positions correspond to the bulk coordinates, or should they correspond to the relaxed coordinates obtained in a calculation without adsorbates?
Thank you.

Hi,

If you need to compare the total energies obtained with the two calculations (one with adsorbates and the other without), then you have to be consistent and make the same choice for both calculations (choose the bulk positions or relax the positions).

If you don't really need the calculation without adsorbates, then which positions to use is more a question of taste. In this respect, what is usually done in studies published in the literature?

Hi Veronika,

I normally relaxed all atoms for the bare slab, fixed one side later and took the other one for the adsorbate.
You'll gain minimum forces at the fixed/not-fixed interface in the slab, which is good for a later frequency analysis (less imaginary modes).

Best regards,

alex

Thank you all.