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remake dopedxpy-sc-fermi #46

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remake dopedxpy-sc-fermi #46

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alexsquires
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@alexsquires alexsquires commented Jan 10, 2024

  • 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
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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
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alexsquires commented Feb 15, 2024 via email

@alexsquires
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@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
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@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 alexsquires marked this pull request as ready for review February 27, 2024 17:17
# Conflicts:
#	examples/CdTe/CdTe_example_thermo.json
# Conflicts:
#	docs/Dev_ToDo.md
@kavanase
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kavanase commented Sep 4, 2024

@alexsquires, I was looking again at the current code in this PR (hopefully nearly ready to go 🤞) as I'm currently trying to use it in some of my work (on selenium defects). I was hoping to use the py-sc-fermi use case where one can set a fixed concentration of a defect/impurity species, and solving with this constraint, but I think this is not implemented as far as I can tell?

I checked back and this was mentioned way back at the start of this PR, and the effective_dopant_concentration option was then added, but I think this other functionality wasn't?

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?

Just checking I'm not missing something / avoiding redundant work. I can add this to the code if it's not there.

@alexsquires
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@alexsquires, I was looking again at the current code in this PR (hopefully nearly ready to go 🤞) as I'm currently trying to use it in some of my work (on selenium defects). I was hoping to use the py-sc-fermi use case where one can set a fixed concentration of a defect/impurity species, and solving with this constraint, but I think this is not implemented as far as I can tell?

I checked back and this was mentioned way back at the start of this PR, and the effective_dopant_concentration option was then added, but I think this other functionality wasn't?

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?

Just checking I'm not missing something / avoiding redundant work. I can add this to the code if it's not there.

I think it would be nice to maybe have it accept a dictionary of defects and concentraitons, and optionally a charge state so e.g.

fixed_concentrations = {"v_Cd": x, "v_Te_+1" : y}

This could fairly easily be an additional kwarg of any of the py-sc-fermi methods?

@alexsquires something I was also thinking about. Do you think it still makes sense to have this under the separate interface module? Of course py-sc-fermi is one of the optional backends here, but most of the code is backend-agnostic. What about moving it into doped.thermodynamics? I don't have any strong feelings about this, just thinking if it's the better category fit

I also thinks this makes sense. I will fix everything up at the beginning of next week, then we could consider moving it?

@kavanase
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Sounds good!

@alexsquires
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Do you have a local version of the example notebook that is not pushed? There are some issues running the version on GH? I can fix them if not, just checking I'm not reinventing the wheel

@kavanase
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As far as I can tell, my local version isn't different to the pushed version, but in case there's any formatting/etc issues, this is my local version, as well as another notebook I was using for some quick tests before.
Archive.zip

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

@kavanase
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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
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Migration finished! Just updating the tests.

alexsquires and others added 10 commits October 17, 2024 17:08
# Conflicts:
#	.github/workflows/pip_install_test.yml
#	.github/workflows/test.yml
#	docs/Dev_ToDo.md
#	examples/CompetingPhases/MgO/MgO_Fm-3m_EaH_0/vasp_std/vasprun.xml
#	examples/CompetingPhases/MgO/MgO_Fm-3m_EaH_0/vasp_std/vasprun.xml.gz
#	examples/CompetingPhases/MgO/Mg_Fm-3m_EaH_0/vasp_std/vasprun.xml
#	examples/CompetingPhases/MgO/Mg_Fm-3m_EaH_0/vasp_std/vasprun.xml.gz
#	examples/CompetingPhases/MgO/Mg_P6_3mmc_EaH_0.009/vasp_std/vasprun.xml
#	examples/CompetingPhases/MgO/Mg_P6_3mmc_EaH_0.009/vasp_std/vasprun.xml.gz
#	examples/CompetingPhases/MgO/Mg_R-3m_EaH_0.003/vasp_std/vasprun.xml
#	examples/CompetingPhases/MgO/Mg_R-3m_EaH_0.003/vasp_std/vasprun.xml.gz
#	examples/CompetingPhases/MgO/O2_mmm_EaH_0/vasp_std/vasprun.xml
#	examples/CompetingPhases/MgO/O2_mmm_EaH_0/vasp_std/vasprun.xml.gz
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