Parsing vacancy complexes

martisby · April 13, 2026, 3:33pm

Hi!

I’m having issues parsing charge states of the divacancy defect complex in AlN (I’m getting a StopIteration error). From what I have gathered from parsing.py it seems that only “substitution”, “vacancy” and “interstitial” are accounted for, and that divacancies hence are not.

Is this correct, or should it be possible to parse such a complex using the DefectsParser?

If it is not possible as of now, is this functionality something you will implement in the future?

Thanks!

kavanase · April 13, 2026, 4:16pm

Hi,
Thanks for raising this. Yes at present DefectsParser in the main code branch is setup to only expect point defects, and not complexes. Full support for complex defect parsing (& generation) is one of the next goals on the development to-do list (with some work planned for this summer), but not yet implemented.

There is some code for handling and parsing defect complexes in the split-vacancies branch: Split Vacancies and Foundation Defect Complexes Code by kavanase · Pull Request #127 · SMTG-Bham/doped · GitHub
Where there are functions for automatically determining the positions and types of complex defects, but the full parsing workflow has not yet been implemented.

There is some discussion of potential workaround approaches here:

github.com/SMTG-Bham/doped

Can doped parse defect complex calculations?

opened 07:09AM - 19 Mar 25 UTC

closed 10:25AM - 27 Mar 25 UTC

jumpingfermions

question

It seems the examples are always about single site defect, e.g. a vacancy or an …interstitial. If I prepare VASP calculations about defect complex such as two neighboring vacancies, can doped recognizes the results, processes further, and plots transition level diagrams? Thank you! Before taking developer time, I have searched the following curated resources for answers: - [x] [`doped` documentation site](https://doped.readthedocs.io) – tip: use the search bar on the left. - [x] [`doped` tutorials](https://doped.readthedocs.io/en/latest/Tutorials.html) - [x] [`doped` Python API docs](https://doped.readthedocs.io/en/latest/doped.html) - [x] [Previous `doped` issues](https://github.com/SMTG-Bham/doped/issues?q=is%3Aissue+is%3Aclosed) where the same question may have been asked – tip: use the search bar. - [ ] All other `doped` docs pages; such as [Tips](https://doped.readthedocs.io/en/latest/Tips.html), [Troubleshooting](https://doped.readthedocs.io/en/latest/Troubleshooting.html) and [Installation](https://doped.readthedocs.io/en/latest/Installation.html) If your question is about general defect calculation methodology (rather than specific to `doped`), please refer to the following papers, and other relevant literature: - [Quick-Start Guide on Defect Calculations – Kim et al.](doi.org/10.1088/2515-7655/aba081) - [Large Review on Defect Calculations – Freysoldt et al.](doi.org/10.1103/RevModPhys.86.253) - [Defect Structure Searching – Mosquera-Lois et al.](doi.org/10.1038/s41524-023-00973-1) - [Free Energies of Defects – Mosquera-Lois et al.](https://doi.org/10.1039/D3CS00432E)

Depending on your use case, you might just want to use e.g. the finite-size correction functions in doped directly (in which case the docs site would be a good place to look), or if you want full parsing and downstream functionality (e.g. thermodynamics modelling), then the discussed workaround may be the best option for now.

martisby · April 15, 2026, 7:50am

Hi,

Thank you for the quick reply! I’m looking forward to the full support for complexes, and in the mean time I’ll check out the workaround.