Cell size on adsorption calculations


I am currently learning how to use ASE and GPAW for doing some adsorption calculations of alkali metals on graphene. I am considering only 2 carbon atoms and 1 adatom (Li or K) for doing this, so my cell is quite small.

When placing the alkali metal above the graphene lattice I saw almost half of the adatom outside of the cell, does this affect the potential energy calculations and further results?

Screen Shot 2021-07-02 at 3.19.52 PM

I tried increasing the size of the cell (so all atoms are inside) but then I’m not able to maintain the correct distances between carbon atoms. Is there any way of doing this? Or, what can be a possible solution for this?

Thanks in advance for your responses :slight_smile:


Repeat the cell until there’s enough space to fit the adsorbate.

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To elaborate, indeed, if the box is small and the atom is large, the calculation will be wrong. Repeat the substrate and then add the adsorbate afterwards. If it’s done right, you should be able to recreate the structure in the example above and see enough space for the atom.

In case there’s any doubt, it’s important to converge the quantity you want with the respect to the number of repetitions, so it’s certain that the periodic images of the adsorbate are not interacting.

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