How to use `extrinsic` to generate deuterium/OH/ions defects? about doped

[kavanase]

HI @Nour-Aldein2!
Yes for deuterium and oxygen substitution, you just need to specify these as extrinsic species for your material using the extrinsic parameter. Deuterium is the same as Hydrogen when it comes to DFT calculations in VASP, apart from MD and phonon calculations where the mass difference matters, and so this can just be set as "H" as such:

(And then if you're following this up with phonon/MD calculations, you would then just need to adjust POMASS in the H POTCAR as discussed here: https://www.vasp.at/forum/viewtopic.php?t=71)

Here you can see it has also generated the O-on-Si substitution you mentioned, in a range of possible charge states (which you can also adjust if needed).

For OH substitution, because this is a complex and it would involve some choice of how the OH molecule is oriented, this is not automated in doped. I would suggest you take the corresponding oxygen interstitial/substitution defect supercell generated by doped, and then manually place H where you expect it to be (or trial a few different configurations). There are many tools for this, and can be done fairly easily within the pymatgen objects from doped. You could then use these structures with the DefectDictSet object from doped.vasp to generate the corresponding input files, or generate them manually / copy from other defects and update NELECT & NUPDOWN accordingly.

Also just to note in general, if you are having some issue with the code, please share an example of what the actual issue is (instead of "that did not work"), as unfortunately I'm not psychic so can't diagnose a specific issue based on just that.

Hope that helps!

[kavanase]

Hi @Nour-Aldein2,
Yes this is entirely possible, and is what is shown in my screenshot above (and in the tutorials on the docs). You just need to provide your Si matrix structure and specify extrinsic= "O" (as shown above), then doped will generate this defect (amongst other possibilities) and give a set of "guessed" likely charge states.
You can then add/remove charge states with the DefectsGenerator.add/remove_charge_states() method as shown in the generation tutorial, if desired.

[kavanase]

Just to note, O_Si^+1 sounds like quite an unlikely charge state.
While I don't agree with some of their message, it might be worth a ready of this paper which discusses the differences between absolute and relative defect charges (we always use relative): https://www.nature.com/articles/s41563-023-01583-4
And then this paper is the classic review on general defect calculations: 10.1103/RevModPhys.86.253

[Nour-Aldein2]

Hi @kavanase,

Thank you for your answer. I apologise if my question was not clear. I'm interested in understanding if it's feasible to explore the various charge states of an ionized oxygen defect, specifically $O^+$, instead of a neutral oxygen atom, within a silicon matrix. Is it possible to generate and investigate the defect $[O^+_{Si}]^q$ with doped, where an oxygen ion substitutes a silicon atom, and $q$ denotes the defect's overall charge state?

Thank you in advance.

[Nour-Aldein2]

Thank you for your answer, @kavanase. I will close this issue for now, and if there's anything in the future, I hope you don't mind if I reopen it.