Notes and minor cleanup

docs/Dev_ToDo.md

@@ -1,6 +1,6 @@
 # `doped` Development To-Do List
 ## Chemical potential
-- Check through chemical potential TO-DOs. Need to recheck validity of approximations used for extrinsic competing phases (and code for this). Proper `vasp_std` setup (with `NKRED` folders like for defect calcs) and `vasp_ncl` generation.
+- Need to recheck validity of approximations used for extrinsic competing phases (and code for this). Proper `vasp_std` setup (with `NKRED` folders like for defect calcs) and `vasp_ncl` generation.
 - Efficient generation of competing phases for which there are many polymorphs? See SK notes from CdTe competing phases.
 - Publication ready chemical potential diagram plotting tool as in Adam Jackson's `plot-cplap-ternary` (3D) and Sungyhun's `cplapy` (4D) (see `doped_chempot_plotting_example.ipynb`; code there, just needs to be implemented in module functions). `ChemicalPotentialGrid` in `py-sc-fermi` interface could be quite useful for this? (Worth moving that part of code out of `interface` subpackage?) Also can see https://github.com/materialsproject/pymatgen-analysis-defects/blob/main/pymatgen/analysis/defects/plotting/phases.py for 2D chempot plotting.
  - Also see `Cs2SnTiI6` notebooks for template code for this.
@@ -15,6 +15,8 @@
  - Could also add an optional right-hand-side y-axis for defect concentration (for a chosen anneal temp) to our TLD plotting (e.g. `concentration_T = None`) as done for thesis, noting in docstring that this obvs doesn't account for degeneracy! 
  - Separate `dist_tol` for interstitials vs (inequivalent) vacancies/substitutions? (See Xinwei chat) Any other options on this front?
  - Also see Fig. 6a of the `AiiDA-defects` preprint, want plotting tools like this
+- Kumagai GKFO and CC diagram corrections. Implemented in `pydefect` and relatively easy to port?
+- 2D corrections; like `pydefect_2d`, or recommended to use SCPC in VASP?
 - Can we add an option to give the `pydefect` defect-structure-info output (shown here https://kumagai-group.github.io/pydefect/tutorial.html#check-defect-structures) – seems quite useful tbf
 
 ## Housekeeping

docs/Future_ToDo.md

@@ -84,9 +84,9 @@
  - In these cases, will also want to be able to plot these in a smart manner on the defect TLD.
  Separate lines to the stoichiometrically-equivalent (unperturbed) point defect, but with the same
  colour just different linestyles? (or something similar)
-- `doped` functions should be equally applicable to the base `pymatgen` `Defect`/`DefectEntry` objects (as well as the corresponding `doped` subclasses) as much as possible. Can we add some quick tests for this? 
 - Implement shallow donor/acceptor binding estimation functions (via effective mass theory)
 - Kasamatsu formula for defect concentrations at high concentrations (accounts for lattice site competition), as shown in DefAP paper
+- Eigenvalue corrections for the eigenvalue plots, like shown in 10.1103/PhysRevB.109.054106?
 
 ## Docs
 - Add LDOS plotting, big selling point for defects and disorder!

doped/thermodynamics.py

@@ -430,7 +430,7 @@ def __init__(
  plots.
 
  Args:
- defect_entries ([DefectEntry] or {str: DefectEntry}):
+ defect_entries (list[DefectEntry] or dict[str, DefectEntry]):
  A list or dict of DefectEntry objects. Note that ``DefectEntry.name``
  attributes are used for grouping and plotting purposes! These should
  be in the format "{defect_name}_{optional_site_info}_{charge_state}".

tests/test_chemical_potentials.py

@@ -529,11 +529,11 @@ def test_structure_input(self, api_key):
 
  _check_structure_input(cp, cp_struct_input, struct, name, w, api_key, extrinsic=True)
 
- for entries_list in [cp_struct_input.entries, cp.entries]:
- assert len(entries_list) >= 1
- for extrinsic_entry in entries_list:
- assert "K" in extrinsic_entry.data["doped_name"]
- assert "K" in extrinsic_entry.name
+  for entries_list in [cp_struct_input.entries, cp.entries]:
+  assert len(entries_list) >= 1
+  for extrinsic_entry in entries_list:
+  assert "K" in extrinsic_entry.data["doped_name"]
+  assert "K" in extrinsic_entry.name
 
 
 class ChemPotAnalyzerTestCase(unittest.TestCase):