Removing atoms repeated on periodic boundaries

[Dawid das]

Dear All,

I am new to molecular modelling of metal oxide systems. What I am trying to do is to obtain a spherical nanoparticle of let's say TiO2 starting from the crystal unit cell (either primitive or conventional).

Now, the issue I find with Vesta is that it i) includes atoms outside unit cell bonded to atoms within unit cell and ii) atoms repeated on periodic boundaries.

This leads to a non-stiochiometric system and I don't want to calculate properties of such clusters. I know how to solve the first issue using Edit--->Bonds, but what about the second one? I tried some tutorials on YT but I can't find a satisfactory solution. On the other hand, it is possible to remove all those
issue in materials project studio for a unit cell, however, Vesta will include these non-stochiometric atoms once I upload the cif file.

Simply speaking, how can I obtain a stochiometric cluster composed of repeated unit cells, please?

Best wishes,

Dawid

[Micah Prange]

One way to avoid seeing multiple images of atoms on the surface of the unit cell is to set the boundary (via the 'boundary' button in the panel on the left) to an interval slightly less than 1 (like 0-0.99) in each of the three cell directions. Also, as you pointed out, turn off the search for bonds outside the cell. The number of atoms drawn will be reported in the text area. If every atom is displayed exactly once the number at atoms reported in the text box will match the number of atoms in the unit cell. You can count the number of atoms in the unit  cell by exporting the structure to a format that lists all the atoms explicitly (e.g. the vasp format).

HTH,

Micah

[Dawid das]

Thank you Micah. That's what I was looking for.