When I created a cif file with hydrogen adsorbed on Ta5n6, I am not able to bind hydrogen to any particular atom, can someone please suggest what should be changed?
Also how to identify if the hydrogen is binded to a particular site? Like top or bridge or hollow ?
I believe you can specify what kinds of sites adsorption site finder uses: see docs
Using the positions argument to find_adsorption_sites
Thank you ardunn for your suggestion!
any idea why i was not able to see a bond between hydrogen and my slab in vesta ?
Hmm I am not sure as I’m not a power user of VESTA. It might have something to do with VESTA’s bonding algorithm? It might be worth manually checking the distance of the H site to the nearest sites in pymatgen/python and ensuring the “bonds” you expect have distances that would normally be shown in vesta as “bonds”.
i.e., if your atom is for some reason not equidistant from at least 2 near sites, it may not show as bonded?
Alternatively, IIRC vesta has options for displaying bonds depending on the unit cell or something, it might be worth messing with those controls as well
@ioandriuc Dear Oxana Andriuc,
I have started to make these slabs following your presentation on youtube. Can you please help me out, if possible?
Seconding @ardunn’s answers above. Each visualization software has its own criteria for deciding which interatomic distances to display as bonds (this information is not explicitly present in the structure file). In Vesta you can edit the maximum distances for displaying bonds for all pairs of elements under Edit → Bonds… If you are hoping to make structures with H covalently bonded to surface atoms this could also be an indication that the H atom is placed too far from the surface, so you might want to adjust the distance parameter when generating the adsorption structures.
