I would like to simulate the adsorbtion of a single molecule on top of a metallic surface.
I thought to create a supercell from a structure object. I could generate the supercell from a file.cif
sxc = Structure.from_file("myfile.cif") sxc.make_supercell([5,5,1])
How can I extend the cell in the z direction? How to add one molecule only?
Alternatiely, I could use the pymatgen.analysis.adsorption module, as demonstrated in this tutorial, but how do I adsorb only one molecule only?