remake dopedxpy-sc-fermi

[alexsquires]

• rename bulk_vasprun, not clear that this needs to be for a high quality dos
• use _format_defect_name() in examples (is this still a private function? If it's externally useful, should it be changed?).
• remove ..._and_save() from FermiSolver methods
• defect_levels argument when annealing becomes a boolean
• docstrings
• multiprocessings
• tests
• suppress noisy warnings
• tutorials
• grid-searching
• effective dopant response
• "exceptions" for FermiSolverPyScFermi

[kavanase]

Looking good @alexsquires. I like the mix-in/abstract class approach.

The _interpolate_chempots() function is quite nice, and I think will likely be one of the mostly-used features from these additions. From what we were discussing before in the #doped Slack, would it be possible to also integrate a grid-scanning approach too? As in, the current function linearly interpolates between two points (chem pot limits), which is nice and v useful in many cases, but if for instance we have a 3D chemical potential space, our min/max of the property of interest could also lie somewhere in the middle of this space, rather than along any linear path between two vertices/limits.

Ofc the user could iterate over all possible vertex/limit combinations if they knew what they were doing, which would be a good stab at this and get you most of the way there I imagine (kind of like a 'band structure path' approach), but still is only covering certain 'high-symmetry' paths in chem pot space. So if a grid approach was also possible (where e.g. the user can just set the chempot spacing in eV, or total number of grid points), that would also be v nice I think – should be doable with some of the scipy grid space interpolation functions I think? And/or pymatgen chemical potential diagram methods maybe?
If it was possible to implement relatively painlessly, could we add these two options? ☝️ 🙏

Sorry to be piling on the requests, but I guess the other main use case I'd imagine for this part of the code would be for the more complex defect thermodynamics analysis that py-sc-fermi allows, where you want to fix certain defect/species etc concentrations and perform some constrained solutions. Is it possible to integrate this to the fermi_solver code?

Also just fyi, about your earlier _format_defect_name() question, yes it is actually quite externally useful and I'll make it a public function in the next (minor) release.

[alexsquires]

Yeah, dw this is all on the list, should be ready to go by the end of the week, I sort of trashed everything to start again (for about the 6th time now), and just adding everything back in piecewise to make sure it's all consistent with the latest thermodynamics object.

…

On Thu, 15 Feb 2024 at 04:58, Seán Kavanagh ***@***.***> wrote: Looking good @alexsquires <https://github.com/alexsquires>. I like the mix-in/abstract class approach. The _interpolate_chempots() function is quite nice, and I think will likely be one of the mostly-used features from these additions. From what we were discussing before in the #doped Slack, would it be possible to also integrate a grid-scanning approach too? As in, the current function linearly interpolates between two points (chem pot limits), which is nice and v useful in many cases, but if for instance we have a 3D chemical potential space, our min/max of the property of interest could also lie somewhere in the middle of this space, rather than along any linear path between two vertices/limits. Ofc the user could iterate over all possible vertex/limit combinations if they knew what they were doing, which would be a good stab at this and get you most of the way there I imagine (kind of like a 'band structure path' approach), but still is only covering certain 'high-symmetry' paths in chem pot space. So if a grid approach was also possible (where e.g. the user can just set the chempot spacing in eV, or total number of grid points), that would also be v nice I think – should be doable with some of the scipy grid space interpolation functions I think? And/or pymatgen chemical potential diagram methods maybe? If it was possible to implement relatively painlessly, could we add these two options? ☝️ 🙏 Sorry to be piling on the requests, but I guess the other main use case I'd imagine for this part of the code would be for the more complex defect thermodynamics analysis that py-sc-fermi allows, where you want to fix certain defect/species etc concentrations and perform some constrained solutions. Is it possible to integrate this to the fermi_solver code? Also just fyi, about your earlier _format_defect_name() question, yes it is actually quite externally useful and I'll make it a public function in the next (minor) release. — Reply to this email directly, view it on GitHub <#46 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AFMK74XGZEUFF3TPF7MZHH3YTXZ5JAVCNFSM6AAAAABBVDPFSSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSNBVHE2TIMRVHE> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[alexsquires]

@adair-nicolson , could you re-parse your Cu2SiSe3 data now that everything is relatively final and I can add the grid searching stuff back in?

[alexsquires]

@kavanase proposing this as the full functionality - do you want to take a look at the example ipynb while I finish off the tests before I get to comfortable?

[alexsquires]

This covers the bug features and feature requests. Do you want to consider the merge into thermodynamics?

[kavanase]

Ok great! Yes let's merge to doped.thermodynamics – and for the ChemicalPotentialGrid code, does it make sense to put it in doped.chemical_potentials?

[alexsquires]

Migration finished! Just updating the tests.