Unexpected Graphene Expansion in VESTA

[Rumana Hasan]

Hello,

I am trying to model a system where the cluster is on top of the Si+graphene interface.

When I open the file  interface_cluster_H.vasp in VESTA the graphene sheet expands in both x and y direction which I don't expect. But in the same file if I replace the chemical element H with B (interface_cluster_B.vasp) the graphene sheet will not expand in x and y direction which is so interesting. Two files are attached herewith.

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Rumana

[Stefano Battaglia]

I have a similar issue with VESTA 3.5.8 on Linux, though for a .cif file. This happens after I open a unit cell of graphene, transform it to replicate it and add atoms at all site positions, then add an adatom on top of the graphene, and then save it as a cif file.

The weird part is that the cif file contains only the right number of atoms, and if I open the file with another software, I only see the supercell I created. In VESTA, on the other hand, it extends on the x and y planes a number of times.

[Micah Prange]

VESTA is probably displaying bonded atoms across the cell boundary. Look at the bonds you have defined (Edit --> Bonds) -- for each bond you can set bonded atoms that would not otherwise be displayed to be included or not (the options are pretty clearly described, and, thankfully, vesta puts some bonds in by default).

[Rumana Hasan]

Thank you for the clarification.

In the Edit > Bonds section I selected the C-C bond and checkmark to " Do not search atoms beyond the boundary" which solved the problem.

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Rumana

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