Adding one H2 molecule on top of a slab

pymatgen
,
1

Hello,
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?

http://matgenb.materialsvirtuallab.org/2018/07/24/Adsorption-on-solid-surfaces.html

Thanks

1 Like