Merge branch 'refs/heads/develop' into dopey_fermi

# Conflicts: # examples/CompetingPhases/MgO/MgO_EaH_0.0/vasp_std/vasprun.xml # examples/CompetingPhases/MgO/MgO_EaH_0.0/vasp_std/vasprun.xml.gz # examples/CompetingPhases/MgO/Mg_EaH_0.0/vasp_std/vasprun.xml # examples/CompetingPhases/MgO/Mg_EaH_0.0/vasp_std/vasprun.xml.gz # examples/CompetingPhases/MgO/Mg_EaH_0.0061/vasp_std/vasprun.xml # examples/CompetingPhases/MgO/Mg_EaH_0.0061/vasp_std/vasprun.xml.gz # examples/CompetingPhases/MgO/Mg_EaH_0.0099/vasp_std/vasprun.xml # examples/CompetingPhases/MgO/Mg_EaH_0.0099/vasp_std/vasprun.xml.gz # examples/CompetingPhases/MgO/O2_EaH_0.0/vasp_std/vasprun.xml # examples/CompetingPhases/MgO/O2_EaH_0.0/vasp_std/vasprun.xml.gz # pyproject.toml
SMTG-Bham · Aug 16, 2024 · da06266 · da06266
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diff --git a/README.md b/README.md
@@ -31,14 +31,8 @@ displacements from DFT supercell calculations. See the [JOSS paper](https://doi.
 ## Installation
 ```bash
 pip install doped # install doped and dependencies
-conda install -c conda-forge spglib # bundle C libraries with spglib
 ```
 
-Note that either `conda install -c conda-forge spglib` or
-`pip install git+https://github.com/spglib/spglib --config-settings=cmake.define.SPGLIB_SHARED_LIBS=OFF`
-should be used after `pip install doped`, which ensures that the correct C libraries are bundled with
-`spglib`, to prevent unnecessary warnings.
-
 Alternatively if desired, `doped` can also be installed from `conda` with:
 
 ```bash
@@ -64,9 +58,10 @@ As shown in the `doped` tutorials, it is highly recommended to use the [`ShakeNB
 Not currently cited but should be for chempot plot:
 - Quadir et al. **_Low-Temperature Synthesis of Stable CaZn<sub>2</sub>P<sub>2</sub> Zintl Phosphide Thin Films as Candidate Top Absorbers_** [_arXiv_](https://arxiv.org/abs/2406.15637) 2024
 -->
+- M. Elgaml et al. **_Controlling the Superconductivity of Nb<sub>2</sub>Pd<sub>x</sub>S<sub>5</sub> via Reversible Li Intercalation_** [_Inorganic Chemistry_](https://pubs.acs.org/doi/full/10.1021/acs.inorgchem.3c03524) 2024
 - Z. Yuan & G. Hautier **_First-principles study of defects and doping limits in CaO_** [_Applied Physics Letters_](https://doi.org/10.1063/5.0211707) 2024
 - B. E. Murdock et al. **_Li-Site Defects Induce Formation of Li-Rich Impurity Phases: Implications for Charge Distribution and Performance of LiNi<sub>0.5-x</sub>M<sub>x</sub>Mn<sub>1.5</sub>O<sub>4</sub> Cathodes (M = Fe and Mg; x = 0.05–0.2)_** [_Advanced Materials_](https://doi.org/10.1002/adma.202400343) 2024
-- A. G. Squires et al. **_Oxygen dimerization as a defect-driven process in bulk LiNiO2<sub>2</sub>_** [_ChemRxiv_](https://doi.org/10.26434/chemrxiv-2024-lcmkj) 2024
+- A. G. Squires et al. **_Oxygen dimerization as a defect-driven process in bulk LiNiO2<sub>2</sub>_** [_ACS Energy Letters_](https://pubs.acs.org/doi/10.1021/acsenergylett.4c01307) 2024
 - Y. Fu & H. Lohan et al. **_Factors Enabling Delocalized Charge-Carriers in Pnictogen-Based
 Solar Absorbers: In-depth Investigation into CuSbSe<sub>2</sub>_** [_arXiv_](https://doi.org/10.48550/arXiv.2401.02257) 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

diff --git a/docs/Dev_ToDo.md b/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

diff --git a/docs/Future_ToDo.md b/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!

diff --git a/docs/Installation.rst b/docs/Installation.rst
@@ -6,22 +6,6 @@ Installation
 .. code-block:: bash
 
  pip install doped # install doped and dependencies
- conda install -c conda-forge spglib # bundle C libraries with spglib
-
-Note that either ``conda install -c conda-forge spglib`` or
-``pip install git+https://github.com/spglib/spglib --config-settings=cmake.define.SPGLIB_SHARED_LIBS=OFF``
-should be used after ``pip install doped``, which ensures that the correct C libraries are bundled with
-``spglib``, to prevent unnecessary warnings. You can check that the correct C libraries have been bundled
-by running the following in Python, and confirming that the same version numbers are printed:
-
-.. code-block:: python
-
- import spglib
- print(spglib.__version__)
- print(spglib.spg_get_version_full())
-
-In some cases, you might need to first uninstall ``spglib`` with both ``conda uninstall spglib`` and
-``pip uninstall spglib`` (to ensure no duplicate installations), before reinstalling.
 
 Alternatively if desired, ``doped`` can also be installed from ``conda`` with:
 

diff --git a/docs/Troubleshooting.rst b/docs/Troubleshooting.rst
@@ -76,11 +76,7 @@ A known issue with ``spglib`` is that it can give unnecessary errors or warnings
  spglib: get_bravais_exact_positions_and_lattice failed
  spglib: ref_get_exact_structure_and_symmetry failed.
 
-This can be fixed by reinstalling ``spglib`` with ``conda install -c conda-forge spglib`` or
-``pip install git+https://github.com/spglib/spglib --config-settings=cmake.define.SPGLIB_SHARED_LIBS=OFF``
-as detailed in the `Installation <https://doped.readthedocs.io/en/latest/Installation.html>`__ instructions.
-This ensures the correct C libraries are bundled with ``spglib``.
-
+Typically this can be fixed by updating to ``spglib>=2.5`` with `pip install --upgrade spglib``.
 .. see doped_spglib_warnings.ipynb
 
 ``ShakeNBreak``

diff --git a/docs/index.rst b/docs/index.rst
@@ -92,9 +92,10 @@ Studies using ``doped``, so far
 .. Not currently cited but should be for chempot plot:
  Quadir et al. **_Low-Temperature Synthesis of Stable CaZn<sub>2</sub>P<sub>2</sub> Zintl Phosphide Thin Films as Candidate Top Absorbers_** [_arXiv_](https://arxiv.org/abs/2406.15637) 2024
 
-- Z\. Yuan & G. Hautier **First-principles study of defects and doping limits in CaO** `Applied Physics Letters <https://doi.org/10.1063/5.0211707>`_ 2024
+- M\. Elgaml et al. **Controlling the Superconductivity of Nb** :sub:`2` **Pd** :sub:`x` **S** :sub:`5` **via Reversible Li Intercalation** `Inorganic Chemistry <https://pubs.acs.org/doi/full/10.1021/acs.inorgchem.3c03524>`__ 2024
+- Z\. Yuan & G. Hautier **First-principles study of defects and doping limits in CaO** `Applied Physics Letters <https://doi.org/10.1063/5.0211707>`__ 2024
 - B\. E. Murdock et al. **Li-Site Defects Induce Formation of Li-Rich Impurity Phases: Implications for Charge Distribution and Performance of LiNi** :sub:`0.5-x` **M** :sub:`x` **Mn** :sub:`1.5` **O** :sub:`4` **Cathodes (M = Fe and Mg; x = 0.05–0.2)** `Advanced Materials <https://doi.org/10.1002/adma.202400343>`_ 2024
-- A\. G. Squires et al. **Oxygen dimerization as a defect-driven process in bulk LiNiO₂** `ChemRxiv <https://doi.org/10.26434/chemrxiv-2024-lcmkj>`__ 2024
+- A\. G. Squires et al. **Oxygen dimerization as a defect-driven process in bulk LiNiO₂** `ACS Energy Letters <https://pubs.acs.org/doi/10.1021/acsenergylett.4c01307>`__ 2024
 - Y\. Fu & H. Lohan et al. **Factors Enabling Delocalized Charge-Carriers in Pnictogen-Based Solar Absorbers: In-depth Investigation into CuSbSe<sub>2</sub>** `arXiv <https://doi.org/10.48550/arXiv.2401.02257>`_ 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

diff --git a/doped/__init__.py b/doped/__init__.py
@@ -71,9 +71,6 @@ def _ignore_pmg_warnings():
  # ignore warning about structure charge that appears when getting Vasprun.as_dict():
  warnings.filterwarnings("ignore", message="Structure charge")
 
- # SpglibDataset warning introduced in v2.4.1
- warnings.filterwarnings("ignore", message="dict interface")
-
 
 _ignore_pmg_warnings()
 

diff --git a/doped/analysis.py b/doped/analysis.py
@@ -224,7 +224,6 @@ def defect_from_structures(
  Dictionary of bulk supercell Voronoi node information, for
  further expedited site-matching.
  """
- warnings.filterwarnings("ignore", "dict interface") # ignore spglib warning from v2.4.1
  try:
  def_type, comp_diff = get_defect_type_and_composition_diff(bulk_supercell, defect_supercell)
  except RuntimeError as exc: