Merge pull request #98 from SMTG-Bham/develop

Develop

Author: kavanase

.github/ISSUE_TEMPLATE/question-about-shakenbreak.md

@@ -7,14 +7,23 @@ assignees: ''
 
 ---
 
-I have searched the following curated resources for answers:
+For general questions related to `ShakeNBreak` and defect structure-searching, we ask that you post these on the 
+[`ShakeNBreak` MatSci community forum](https://matsci.org/c/shake-n-break/71).
+
+Before taking developer time, we kindly ask that you first check the following curated resources for answers, as many
+questions have been answered before:
 - [ ] [`ShakeNBreak` documentation site](https://shakenbreak.readthedocs.io/en/latest/) – tip: use the search bar on the left.
 - [ ] [`ShakeNBreak` tutorials](https://shakenbreak.readthedocs.io/en/latest/Tutorials.html)
 - [ ] [`ShakeNBreak` Python API docs](https://shakenbreak.readthedocs.io/en/latest/modules.html)
 - [ ] [Previous `ShakeNBreak` issues](https://github.com/SMTG-Bham/ShakeNBreak/issues?q=is%3Aissue+is%3Aclosed) where the same question may have been asked – tip: use the search bar.
 - [ ] All other `ShakeNBreak` docs pages; such as [Tips](https://shakenbreak.readthedocs.io/en/latest/Tips.html) and [Installation](https://shakenbreak.readthedocs.io/en/latest/Installation.html)
+- [ ] [`ShakeNBreak` MatSci community forum](https://matsci.org/c/shake-n-break/71)
 
 If your question is about general defect structure-searching methodology, please refer to the following papers, and other relevant literature:
 - [Defect Structure Searching Preview](https://doi.org/10.1016/j.matt.2021.06.003)
-- [Defect Structure Searching Main Paper](doi.org/10.1038/s41524-023-00973-1)
+- [Defect Structure Searching Main Paper](https://doi.org/10.1038/s41524-023-00973-1)
+- [Guidelines for Robust Defect Simulations](https://doi.org/10.1038/s41578-025-00879-y)
 - [Free Energies of Defects](https://doi.org/10.1039/D3CS00432E)
+
+FAQ: Why are only `Rattled` and `Unperturbed` generated for some charge states?
+> `ShakeNBreak` uses the change in valence electron count (i.e. 'excess charge') at the defect site to dictate the number of bonds to distort, which was found to be the best chemically-motivated strategy; see [the npj theory paper](https://www.nature.com/articles/s41524-023-00973-1). For _fully-ionised_ charge states (e.g. `v_Cu_-1`) the excess charge is zero, and so no bonds are distorted and only rattling to break symmetry is trialled. These defect charge states are typically the most simple, and do not involve charge localisation.

.github/workflows/test.yml

@@ -1,13 +1,12 @@
 name: Tests
 
 on:
+  workflow_dispatch:
+
   push:
     branches:
       - '*'  # all branches
 
-  workflow_dispatch:
-  pull_request:
-
 jobs:
   test:
     strategy:

.gitignore

@@ -151,3 +151,6 @@ conda_packaging.md
 .pytest_cache/
 shakenbreak/__pycache__/
 tests/__pycache__/
+
+# Cursor
+.cursor/

CHANGELOG.rst

@@ -1,6 +1,15 @@
 Change Log
 ==========
 
+v3.4.4
+----------
+- Update ``doped`` requirement and use latest ``doped`` oxidation state functions.
+- Restrict ``hiphive`` imports to within functions, to reduce dependence on dependencies (primarily
+  ``numba``, which can often lag behind latest ``numpy``).
+- Remove deprecated ``pymatgen`` version check code.
+- Code cleanup, docs updates & minor bugfixes for extreme edge cases.
+
+
 v3.4.3
 ----------
 - Efficient oxidation state guessing using ``doped`` functions, along with handling of mixed-valence systems by @hwbng
@@ -144,9 +153,10 @@ v3.2.0
 ----------
 - Following the major release of ``doped`` ``v2.0``, now compatible with the new ``pymatgen``
   defects code (``pymatgen>2022.7.25``), this update:
-    - Allows input of ``doped`` ``DefectsGenerator`` object to ``Distortions``
-    - Updates the tutorials to reflect the current recommended workflow of generating defects
-      with ``doped`` and then applying ``ShakeNBreak``, no longer requiring separate virtual environments 🎉
+
+  - Allows input of ``doped`` ``DefectsGenerator`` object to ``Distortions``
+  - Updates the tutorials to reflect the current recommended workflow of generating defects
+    with ``doped`` and then applying ``ShakeNBreak``, no longer requiring separate virtual environments 🎉
 
 v3.1.0
 ----------
@@ -204,7 +214,7 @@ v23.02.02
 
 
 v23.01.25
---------
+----------
 
 - Specify ``pandas`` version in requirements.txt to equal or higher than 1.1.0
 - Refactor ``snb-regenerate`` to execute when no arguments are specified (rather than showing help message)
@@ -228,7 +238,7 @@ v22.12.1
 
 
 v22.11.29
---------
+----------
 
 - Add example notebook showing how to generate interstitials and apply SnB to them.
 - Fix typo in example notebook and docs.
@@ -237,19 +247,14 @@ v22.11.29
 
 
 v22.11.18
---------
-
-Add docs plots.
-
-
-v22.11.18
---------
+----------
 
-Docs tutorial update.
+(b). Add docs plots.
+(a). Docs tutorial update.
 
 
 v22.11.17
---------
+----------
 
 - Refactor ``Distortions()`` to a list or simple-format dict of ``Defect`` objects as input.
   Same for ``Distortions.from_structures()``
@@ -283,12 +288,12 @@ v22.11.1
 
 
 v22.10.14
---------
+----------
 
 Just bumping version number to test updated GH Actions ``pip-install-test`` workflow.
 
 v22.10.13
---------
+----------
 
 - Updated defect name handling to work for all conventions
 - More robust ``snb-generate`` and plotting behaviour