Update paper list

README.md

@@ -73,11 +73,9 @@ entirely refactored and rewritten, to work with the new
 - P. A. Hyde et al. [_Inorganic Chemistry_](https://doi.org/10.1021/acs.inorgchem.3c01510) 2023
 - J. Willis, K. B. Spooner, D. O. Scanlon. [_Applied Physics Letters_](https://doi.org/10.1063/5.0170552) 2023
 - J. Cen et al. [_Journal of Materials Chemistry A_](https://doi.org/10.1039/D3TA00532A) 2023
-- J. Willis & R. Claes et al. [_ChemRxiv_](https://doi.org/10.26434/chemrxiv-2023-lttnf) 2023
+- J. Willis & R. Claes et al. [_Chem Mater_](https://doi.org/10.1021/acs.chemmater.3c01628) 2023
 - I. Mosquera-Lois & S. R. Kavanagh, A. Walsh, D. O. Scanlon [_npj Computational Materials_](https://www.nature.com/articles/s41524-023-00973-1) 2023
 - Y. T. Huang & S. R. Kavanagh et al. [_Nature Communications_](https://www.nature.com/articles/s41467-022-32669-3) 2022
 - S. R. Kavanagh, D. O. Scanlon, A. Walsh, C. Freysoldt [_Faraday Discussions_](https://doi.org/10.1039/D2FD00043A) 2022
 - S. R. Kavanagh, D. O. Scanlon, A. Walsh [_ACS Energy Letters_](https://pubs.acs.org/doi/full/10.1021/acsenergylett.1c00380) 2021
 - C. J. Krajewska et al. [_Chemical Science_](https://doi.org/10.1039/D1SC03775G) 2021
-
-<!-- Update JPCC CSTX reference! Xinwei PRB? Kumagai paper (was used for defect generation) -->

docs/Dev_ToDo.md

@@ -160,7 +160,7 @@
     Primitive structure can change, as can supercell / supercell matrix (depending on input structure,
     `generate_supercell` etc), but conventional cell should always be the same (`spglib` convention).
   - Add examples of extending analysis with `easyunfold` and `py-sc-fermi`, and get the lads to add
-    this to their docs as example use cases as well. Add our thesis sc-fermi analysis notebooks to tutorials. Also include examples of extending to
+    this to their docs as example use cases as well. Add our thesis sc-fermi analysis notebooks to tutorials, and example of doing the Kumagai PRX Energy carrier concentration with TLD plots (can use: https://py-sc-fermi.readthedocs.io/en/latest/tutorial.html#plot-defect-concentrations-as-a-function-of-Fermi-energy). Also include examples of extending to
     non-radiative carrier capture calcs with `CarrierCapture.jl` and `nonrad`. Show example of using
     `sumo` to get the DOS plot of a defect calc, and why this is useful.
   - Worth adding a very short example showing how to set `MAGMOM`s for AFM/FM systems (see Dan & Abdullah chat)

docs/index.rst

@@ -111,7 +111,7 @@ Studies using ``doped``
 - P\. A. Hyde et al. `Inorganic Chemistry <https://doi.org/10.1021/acs.inorgchem.3c01510>`_ 2023
 - J\. Willis, K. B. Spooner, D. O. Scanlon. `Applied Physics Letters <https://doi.org/10.1063/5.0170552>`__ 2023
 - J\. Cen et al. `Journal of Materials Chemistry A`_ 2023
-- J\. Willis & R. Claes et al. `ChemRxiv <https://doi.org/10.26434/chemrxiv-2023-lttnf>`__ 2023
+- J\. Willis & R. Claes et al. `Chem Mater <https://doi.org/10.1021/acs.chemmater.3c01628>`__ 2023
 - I\. Mosquera-Lois & S. R. Kavanagh, A. Walsh, D. O. Scanlon `npj Computational Materials`_ 2023
 - Y\. T. Huang & S. R. Kavanagh et al. `Nature Communications`_ 2022
 - S\. R. Kavanagh, D. O. Scanlon, A. Walsh, C. Freysoldt `Faraday Discussions`_ 2022

doped/utils/wyckoff.py

@@ -209,8 +209,7 @@ def _rotate_and_get_supercell_matrix(prim_struct, target_struct):
         supercell_matrix = mapping[2]
     rotation_symmop = SymmOp.from_rotation_and_translation(
         rotation_matrix=rotation_matrix.T
-    )  # Transpose = inverse of rotation matrices (orthogonal matrices), better numerical
-    # stability
+    )  # Transpose = inverse of rotation matrices (orthogonal matrices), better numerical stability
     output_prim_struct = prim_struct.copy()
     output_prim_struct.apply_operation(rotation_symmop)
     clean_prim_struct_dict = _round_floats(output_prim_struct.as_dict())