Package: doped
dopedis a python package for
managing solid-state defect calculations, with functionality to
generate defect structures and relevant competing phases (for chemical potentials), interface withShakeNBreakfordefect structure-searching, write VASP input files for defect
supercell calculations, and automatically parse and analyse the results.Tutorials showing the code functionality and usage are provided on thedocssite.Example Outputs:Chemical potential/stability region plots and defect formation energy (a.k.a. transition level) diagrams:Installationpipinstalldoped# install doped and dependenciesAlternatively if desired,dopedcan also be installed fromcondawith:condainstall-cconda-forgedopedIf you haven't done so already, you will need to set up your VASPPOTCARfiles andMaterials ProjectAPI withpymatgenusing the.pmgrc.yamlfile, in order fordopedto automatically generate VASP input files for defect calculations and determine competing phases for chemical potentials.
See the docsInstallationpage for details on this.ShakeNBreakAs shown in the example notebook, it is highly recommended to use theShakeNBreakapproach when calculating point defects in solids, to ensure you have identified the groundstate structures of your defects. As detailed in thetheory paper, skipping this step can result in drastically incorrect formation energies, transition levels, carrier capture (basically any property associated with defects). This approach is followed in thedoped example notebook, with a more in-depth explanation and tutorial given on theShakeNBreakwebsite.Summary GIF:SnBCLI Usage:Acknowledgmentsdoped(néeDefectsWithTheBoys#iykyk) has benefitted from feedback from many users, in particular
members of theScanlonandWalshresearch groups who have used / are using it in their work. Direct contributors are listed in theContributorssidebar above; including Seán Kavanagh, Bonan Zhu, Katarina Brlec, Adair Nicolson,
Sabrine Hachmioune and Savya Aggarwal.Code to efficiently identify defect species from input supercell structures was contributed by DrAlex Ganose, and the colour scheme for defect formation energy plots was originally templated from
theaidepackage, developed by the dynamic duoAdam JacksonandAlex Ganose.Thedocswebsite setup was templated from theShakeNBreakdocs set up byIrea Mosquera-Lois🙌dopedwas originally based on the excellentPyCDT(no longer maintained), but transformed
and morphed over time as more and more functionality was added. After breaking changes inpymatgen, the package was
entirely refactored and rewritten, to work with the newpymatgen-analysis-defectspackage.Studies usingdoped, so farX. Wang et al.arXiv2024I. Mosquera-Lois et al.arXiv2024W. Dou et al.ChemRxiv2024K. Li et al.ChemRxiv2023X. Wang et al.Physical Review B2023Y. Kumagai et alPRX Energy2023S. M. Liga & S. R. Kavanagh, A. Walsh, D. O. Scanlon, G. KonstantatosJournal of Physical Chemistry C2023A. T. J. Nicolson et al.Journal of Materials Chemistry A2023Y. W. Woo, Z. Li, Y-K. Jung, J-S. Park, A. WalshACS Energy Letters2023P. A. Hyde et al.Inorganic Chemistry2023J. Willis, K. B. Spooner, D. O. Scanlon.Applied Physics Letters2023J. Cen et al.Journal of Materials Chemistry A2023J. Willis & R. Claes et al.Chem Mater2023I. Mosquera-Lois & S. R. Kavanagh, A. Walsh, D. O. Scanlonnpj Computational Materials2023Y. T. Huang & S. R. Kavanagh et al.Nature Communications2022S. R. Kavanagh, D. O. Scanlon, A. Walsh, C. FreysoldtFaraday Discussions2022S. R. Kavanagh, D. O. Scanlon, A. WalshACS Energy Letters2021C. J. Krajewska et al.Chemical Science2021