Problems of appearing periodicity for a XSF file with nbound file.
Joint Density Functional Theory
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#28 Problems of appearing periodicity for a XSF file with nbound file.
Hi Shanker,
When I did the exercise of fixed surface potential, I generated xsf and nbound file as instructed, but when visualized in VESTA, I cannot adjust it to be shown periodically, the ions only appears at fixed positions and cannot be seen as normally( in my case Pt and H should bound together). I attached the files in this ticket.( I firstly what to submit this issue in discussion but I found files cannot be attaced there so I have to submit here)
By the way, if I want to add one proton i.e. H+ and let it react with H atom adsorbed on Pt in my case, how can I realize that? What should the form of H+ be in ionpos file?
Thank you very much!
Sincerely,
Yunhao
Hi Yunhao,
I am not sure what you are trying to do here. As far as I can tell, the XSF correctly reproduces the input system you specified: a Pt atom and a H atom in a 10 bohr^3 box. You can adjust the boundary setting to [-0.5,0.5] in each dimension in VESTA to show the Pt and H closer to each other.
Were you trying to put H next to a Pt surface? If so, you need to specify a different geometry which actually contains a Pt surface like in the tutorials. The reason you are not getting the correct periodicity in VESTA is because the input doesn;t have it.
As for your question, add a H to your input file usin the ion command as usual, and then use command elec-initial-charge to specify the net charge of the system. Alternately, if you are doing fixed potential, the electronic charge will automaticlaly adjust. ote that you cannot constrain the charge to be in a specific area; you can only control the net number of electrons in the system. (Also note that elec-initial-charge specifies charge in excess electrons.)
Best,
Shankar