SMTG-Bham · alexsquires · Jan 10, 2024 · Jan 11, 2024 · Jan 11, 2024 · Jan 11, 2024
diff --git a/.gitignore b/.gitignore
@@ -2,6 +2,7 @@
 
 # No PyCharm
 .idea/
+tests/__init__.py
 
 # Ignore Mac Finder metadata file
 .DS_Store

diff --git a/README.md b/README.md
@@ -50,14 +50,15 @@ If you use `doped` in your research, please cite:
 - S. R. Kavanagh et al. [doped: Python toolkit for robust and repeatable charged defect supercell calculations](https://doi.org/10.21105/joss.06433). _Journal of Open Source Software_ 9 (96), 6433, **2024**
 
 ## `ShakeNBreak`
-As shown in the `doped` tutorials, it is highly recommended to use the [`ShakeNBreak`](https://shakenbreak.readthedocs.io/en/latest/) approach when calculating point defects in solids, to ensure you have identified the groundstate structures of your defects. As detailed in the [theory paper](https://doi.org/10.1038/s41524-023-00973-1), 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 the [doped example notebook](https://github.com/SMTG-Bham/doped/blob/main/dope_workflow_example.ipynb), with a more in-depth explanation and tutorial given on the [ShakeNBreak](https://shakenbreak.readthedocs.io/en/latest/) website.
+As shown in the `doped` tutorials, it is highly recommended to use the [`ShakeNBreak`](https://shakenbreak.readthedocs.io/en/latest/) approach when calculating point defects in solids, to ensure you have identified the groundstate structures of your defects. As detailed in the [theory paper](https://doi.org/10.1038/s41524-023-00973-1), 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 the [doped defect generation tutorial](https://doped.readthedocs.io/en/latest/generation_tutorial.html), with a more in-depth explanation and tutorial given on the [ShakeNBreak](https://shakenbreak.readthedocs.io/en/latest/) website.
 
 ![ShakeNBreak Summary](https://raw.githubusercontent.com/SMTG-Bham/ShakeNBreak/main/docs/SnB_Supercell_Schematic_PES_2sec_Compressed.gif)
 
 ## Studies using `doped`, so far
 
+- S. R. Kavanagh **_Identifying Split Vacancies with Foundation Models and Electrostatics_** [_arXiv_](https://doi.org/10.48550/arXiv.2412.19330) 2024
 - S. R. Kavanagh et al. **_Intrinsic point defect tolerance in selenium for indoor and tandem photovoltaics_** [_ChemRxiv_](https://doi.org/10.26434/chemrxiv-2024-91h02) 2024
-- X. Wang et al. **_Sulfur Vacancies Limit the Open-circuit Voltage of Sb<sub>2</sub>S<sub>3</sub> Solar Cells_** [_arXiv_](https://doi.org/10.48550/arXiv.2410.10560) 2024
+- X. Wang et al. **_Sulfur Vacancies Limit the Open-circuit Voltage of Sb<sub>2</sub>S<sub>3</sub> Solar Cells_** [_ACS Energy Letters_](https://doi.org/10.1021/acsenergylett.4c02722) 2024
 - A. Zhang et al. **_Optimizing the n-type carrier concentration of an InVO<sub>4</sub> photocatalyst by codoing with donors and intrinsic defects_** [_Physical Review Applied_](https://doi.org/10.1103/PhysRevApplied.22.044047) 2024
 - M-L. Wang et al. **_Impact of sulfur doping on copper-substituted lead apatite_** [_Physical Review B_](https://doi.org/10.1103/PhysRevB.110.104109) 2024
 - S. Quadir et al. **_Low-Temperature Synthesis of Stable CaZn<sub>2</sub>P<sub>2</sub> Zintl Phosphide Thin Films as Candidate Top Absorbers_** [_Advanced Energy Materials_](https://doi.org/10.1002/aenm.202402640) 2024
@@ -73,6 +74,7 @@ Solar Absorbers: In-depth Investigation into CuSbSe<sub>2</sub>_** [_arXiv_](htt
 - K. Li et al. **_Computational Prediction of an Antimony-based n-type Transparent Conducting Oxide: F-doped Sb<sub>2</sub>O<sub>5</sub>_** [_Chemistry of Materials_](https://doi.org/10.1021/acs.chemmater.3c03257) 2024
 - S. Hachmioune et al. **_Exploring the Thermoelectric Potential of MgB<sub>4</sub>: Electronic Band Structure, Transport Properties, and Defect Chemistry_** [_Chemistry of Materials_](https://doi.org/10.1021/acs.chemmater.4c00584) 2024
 - J. Hu et al. **_Enabling ionic transport in Li<sub>3</sub>AlP<sub>2</sub> the roles of defects and disorder_** [_ChemRxiv_](https://doi.org/10.26434/chemrxiv-2024-3s0kh) 2024
+- Y. Zeng et al. **_Role of carbon in α-Al2O3:C crystals investigated with first-principles calculations and experiment_** [_Ceramics International_](https://doi.org/10.1016/j.ceramint.2024.12.512) 2024
 - X. Wang et al. **_Four-electron negative-U vacancy defects in antimony selenide_** [_Physical Review B_](https://journals.aps.org/prb/abstract/10.1103/PhysRevB.108.134102) 2023
 - Y. Kumagai et al. **_Alkali Mono-Pnictides: A New Class of Photovoltaic Materials by Element Mutation_** [_PRX Energy_](http://dx.doi.org/10.1103/PRXEnergy.2.043002) 2023
 - S. M. Liga & S. R. Kavanagh, A. Walsh, D. O. Scanlon, G. Konstantatos **_Mixed-Cation Vacancy-Ordered Perovskites (Cs<sub>2</sub>Ti<sub>1–x</sub>Sn<sub>x</sub>X<sub>6</sub>; X = I or Br): Low-Temperature Miscibility, Additivity, and Tunable Stability_** [_Journal of Physical Chemistry C_](https://doi.org/10.1021/acs.jpcc.3c05204) 2023

diff --git a/docs/Dev_ToDo.md b/docs/Dev_ToDo.md
@@ -97,6 +97,7 @@
 - - Should have a general refactor from `(bulk, defect)` to `(defect, bulk)` in inputs to functions (e.g. site-matching, symmetry functions etc), as this is most intuitive and then keep consistent throughout.
 - Quick-start tutorial suggested by Alex G
 - Test chempot grid plotting tool.
-- `dist_tol` should also group defects for the concentration etc functions, currently doesn't (e.g. `CdTe_thermo.get_equilibrium_concentrations(limit="Te-rich", per_charge=False, fermi_level=0.5)` and `CdTe_thermo.dist_tol=10; CdTe_thermo.get_equilibrium_concentrations(limit="Te-rich", per_charge=False, fermi_level=0.5)`, same output)
+- `dist_tol` should also group defects for the concentration etc functions, currently doesn't (e.g. `CdTe_thermo.get_equilibrium_concentrations(limit="Te-rich", per_charge=False, fermi_level=0.5)` and `CdTe_thermo.dist_tol=10; CdTe_thermo.get_equilibrium_concentrations(limit="Te-rich", per_charge=False, fermi_level=0.5)`, same output). This also affects the grouping for concentration outputs by the two different `FermiSolver` backends, so keep an eye on this.
 - Add example to chemical potentials / thermodynamics analysis tutorials of varying chemical potentials as a function of temperature/pressure (i.e. gas phases), using the `Spinney` functions detailed here (https://spinney.readthedocs.io/en/latest/tutorial/chemipots.html#including-temperature-and-pressure-effects-through-the-gas-phase-chemical-potentials) or possibly `DefAP` functions otherwise. Xinwei Sb2S3 stuff possibly a decent example for this, see our notebooks.
+- Add note to chempots tutorial that if your bulk phase is lower energy than its version on the MP (e.g. distorted perovskite), then you should use this for your bulk competing phase calculation?
 - Deal with cases where "X-rich"/"X-poor" corresponds to more than one limit (pick one and warn user?)(e.g. Wenzhen Si2Sb2Te6). Can see `get_chempots` in `pmg-analysis-defects` for inspo on this.
diff --git a/docs/Tips.rst b/docs/Tips.rst
@@ -554,11 +554,6 @@ In the typical defect calculation workflow with ``doped`` (exemplified in the tu
   ``DefectsParser(json_filename="custom_name.json")``, but the default is
   ``{Host Chemical Formula}_defect_dict.json``.
 
-    - Additionally, a ``voronoi_nodes.json`` file is saved to the bulk supercell calculation directory if
-      any interstitial defects are parsed. This contains information about the Voronoi tessellation nodes
-      in the host structure, which are used for analysing interstitial positions but can be somewhat costly
-      to calculate – so are automatically saved to file once initially computed to reduce parsing times.
-
 - Additionally, if following the recommended structure-searching approach with ``ShakeNBreak`` as shown in
   the tutorials, ``distortion_metadata.json`` files will be written to the top directory (``output_path``,
   containing distortion information about all defects) and to each defect directory (containing just the
@@ -572,7 +567,7 @@ is not done automatically.
 ^^^^^^^^^^^^^^^^^^^^^
 Many analysis methods in ``doped`` return ``pandas`` ``DataFrame`` objects as the result, such as the
 ``get_symmetries_and_degeneracies()``, ``get_formation_energies()``, ``get_equilibrium_concentrations()``,
-``get_quenched_fermi_level_and_concentrations``, ``get_dopability_limits()``, ``get_doping_windows()`` and
+``get_fermi_level_and_concentrations``, ``get_dopability_limits()``, ``get_doping_windows()`` and
 ``get_transition_levels()`` methods for ``DefectThermodynamics`` objects, and the ``formation_energy_df``
 attribute and ``calculate_chempots()`` method for ``CompetingPhasesAnalyzer``. As mentioned in the
 tutorials, these ``DataFrame`` objects can be output to ``csv`` (or ``json``, ``xlsx`` etc., see the

diff --git a/docs/Tutorials.rst b/docs/Tutorials.rst
@@ -15,5 +15,6 @@ tutorials:
    thermodynamics_tutorial
    chemical_potentials_tutorial
    advanced_analysis_tutorial
+   fermisolver_tutorial
    plotting_customisation_tutorial
    GGA_workflow_tutorial
diff --git a/docs/fermisolver_tutorial.ipynb b/docs/fermisolver_tutorial.ipynb
@@ -0,0 +1 @@
+../examples/fermisolver_tutorial.ipynb
diff --git a/docs/index.rst b/docs/index.rst
@@ -90,8 +90,9 @@ the
 Studies using ``doped``, so far
 ===============================
 
+- S\. R. Kavanagh **Identifying Split Vacancies with Foundation Models and Electrostatics** `arXiv <https://doi.org/10.48550/arXiv.2412.19330>`__ 2024
 - S\. R. Kavanagh et al. **Intrinsic point defect tolerance in selenium for indoor and tandem photovoltaics** `ChemRxiv <https://doi.org/10.26434/chemrxiv-2024-91h02>`__ 2024
-- X\. Wang et al. **Sulfur vacancies limit the open-circuit voltage of Sb₂S₃ solar cells** `arXiv <https://doi.org/10.48550/arXiv.2410.10560>`_ 2024
+- X\. Wang et al. **Sulfur vacancies limit the open-circuit voltage of Sb₂S₃ solar cells** `ACS Energy Letters <https://doi.org/10.1021/acsenergylett.4c02722>`__ 2024
 - A\. Zhang et al. **Optimizing the n-type carrier concentration of an InVO₄ photocatalyst by codoping with donors and intrinsic defects** `Physical Review Applied <https://doi.org/10.1103/PhysRevApplied.22.044047>`__ 2024
 - M-L\. Wang et al. **Impact of sulfur doping on copper-substituted lead apatite** `Physical Review B <https://doi.org/10.1103/PhysRevB.110.104109>`__ 2024
 - S\. Quadir et al. **Low-Temperature Synthesis of Stable CaZn₂P₂ Zintl Phosphide Thin Films as Candidate Top Absorbers** `Advanced Energy Materials <https://doi.org/10.1002/aenm.202402640>`__ 2024
@@ -106,6 +107,7 @@ Studies using ``doped``, so far
 - K\. Li et al. **Computational Prediction of an Antimony-based n-type Transparent Conducting Oxide: F-doped Sb₂O₅** `Chemistry of Materials <https://doi.org/10.1021/acs.chemmater.3c03257>`__ 2024
 - S\. Hachmioune et al. **Exploring the Thermoelectric Potential of MgB₄: Electronic Band Structure, Transport Properties, and Defect Chemistry** `Chemistry of Materials <https://doi.org/10.1021/acs.chemmater.4c00584>`__ 2024
 - J\. Hu et al. **Enabling ionic transport in Li₃AlP₂ the roles of defects and disorder** `ChemRxiv <https://doi.org/10.26434/chemrxiv-2024-3s0kh>`__ 2024
+- Y\. Zeng et al. **Role of carbon in α-Al2O3:C crystals investigated with first-principles calculations and experiment** `Ceramics International <https://doi.org/10.1016/j.ceramint.2024.12.512>`__ 2024
 - X\. Wang et al. **Four-electron negative-U vacancy defects in antimony selenide** `Physical Review B <https://journals.aps.org/prb/abstract/10.1103/PhysRevB.108.134102>`__ 2023
 - Y\. Kumagai et al. **Alkali Mono-Pnictides: A New Class of Photovoltaic Materials by Element Mutation** `PRX Energy <http://dx.doi.org/10.1103/PRXEnergy.2.043002>`__ 2023
 - S\. M. Liga & S. R. Kavanagh, A. Walsh, D. O. Scanlon, G. Konstantatos **Mixed-Cation Vacancy-Ordered Perovskites (Cs₂Ti** :sub:`1–x` **Sn** :sub:`x` **X₆; X = I or Br): Low-Temperature Miscibility, Additivity, and Tunable Stability** `Journal of Physical Chemistry C <https://doi.org/10.1021/acs.jpcc.3c05204>`__ 2023