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I am not asking which software to use to or how to remove atoms from a supercell. But rather how to decide which part should be removed. Like do I give preference to some surfaces or some particular molecules. Currently I am working with a layered material and that is why I am a bit confused. Like do I take the layer into the nano material or not and if I do take it then do I take one layer or two?

I am pretty sure that there exists some logical pointers that must be considered while cutting a structure. And things like make the structure more symmetric are also helpful. Any help is greatly appreciated.

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  • $\begingroup$ I think that the justification about which part should be removed, only after some experimental results or after knowing theoretical calculations about surface energy. $\endgroup$
    – Camps ♦
    Feb 21, 2022 at 11:24
  • $\begingroup$ Such cutting is possible only if you have previous knowledge about the system (stable faces, surface structure) or you have to compare several different model, and decide based on free energy (assuming that the nano system is close to equilibrium somehow). Note that many times the definition of the proper NP itself is a separate study (eg creating realistic TiO2 nanoparticles). $\endgroup$
    – Greg
    Feb 21, 2022 at 23:46
  • $\begingroup$ This question would benefit from more specifics: What is the purpose of this operation? And, ideally, what material are you using? If your goal is to identify layers in a layered material, you can rely on heuristics based on interatomic distances, see e.g. "Identification of compounds containing low-dimensional units" in nature.com/articles/s41565-017-0035-5#Sec6 $\endgroup$
    – leopold.talirz
    Mar 18, 2022 at 18:05
  • $\begingroup$ This question appears to be abandoned. It can be reopened if OP addresses questions/suggestions in the comments. $\endgroup$
    – Tyberius ♦
    Sep 3, 2022 at 2:24

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