Merge pull request #64 from SMTG-Bham/develop

`ShakeNBreak` 3.3.0
SMTG-Bham · Feb 13, 2024 · 7d9b49e · 7d9b49e
2 parents 6e85876 + ad3eadf
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diff --git a/.gitignore b/.gitignore
@@ -150,4 +150,4 @@ snb_test.ipynb
 conda_packaging.md
 .pytest_cache/
 shakenbreak/__pycache__/
-tests/__pycache__/
+tests/__pycache__/
diff --git a/.pytest_cache/.gitignore b/.pytest_cache/.gitignore
diff --git a/.pytest_cache/CACHEDIR.TAG b/.pytest_cache/CACHEDIR.TAG
diff --git a/.pytest_cache/README.md b/.pytest_cache/README.md
diff --git a/.pytest_cache/v/cache/lastfailed b/.pytest_cache/v/cache/lastfailed
diff --git a/.pytest_cache/v/cache/nodeids b/.pytest_cache/v/cache/nodeids
diff --git a/.pytest_cache/v/cache/stepwise b/.pytest_cache/v/cache/stepwise
diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -1,7 +1,7 @@
 Change Log
 ==========
 
-v3.2.4
+v3.3.0
 ----------
 - Add Dimer distortion as a targeted distortion for dimer reconstructions. It pushes two of the defect NN
   to a distance of 2 A.
@@ -17,6 +17,7 @@ v3.2.4
   the user about this (i.e. only `Unperturbed`)
 - Update `snb-run` to add early-on detection of distortions that are stuck in high energy basins and
   rename them to "High_Energy" to avoid continuing their relaxation
+- Miscellaneous efficiency improvements and bug fixes
 
 v3.2.3
 ----------

diff --git a/MANIFEST.in b/MANIFEST.in
@@ -1,3 +1 @@
-include parse*
-recursive-include shakenbreak *
-recursive-include data *
+recursive-include shakenbreak *
diff --git a/README.md b/README.md
@@ -127,7 +127,8 @@ Automatic testing is run on the master and develop branches using Github Actions
 `ShakeNBreak` has benefitted from feedback from many members of the Walsh and Scanlon research groups who have used / are using it in their work, including Adair Nicolson, Xinwei Wang, Katarina Brlec, Joe Willis, Zhenzhu Li, Jiayi Cen, Lavan Ganeshkumar, Daniel Sykes, Luisa Herring-Rodriguez, Alex Squires, Sabrine Hachmioune and Chris Savory.
 
 ## Studies using `ShakeNBreak`
-<!-- Wenzhen, Xinwei papers -->
+
+- X. Wang et al. [_arXiv_](https://arxiv.org/abs/2402.04434) 2024
 - I. Mosquera-Lois et al. [_arXiv_](https://doi.org/10.48550/arXiv.2401.12127) 2024
 - K. Li et al. [_ChemRxiv_](https://chemrxiv.org/engage/chemrxiv/article-details/65846b8366c1381729bc5f23) 2023
 - X. Wang et al. [_Physical Review B_](https://journals.aps.org/prb/abstract/10.1103/PhysRevB.108.134102) 2023
@@ -139,10 +140,12 @@ Automatic testing is run on the master and develop branches using Github Actions
 - I. Mosquera-Lois & S. R. Kavanagh, A. Walsh, D. O. Scanlon [_npj Computational Materials_](https://doi.org/10.1038/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
+- Y-S. Choi et al. [_ACS Appl. Energy Mater._](https://doi.org/10.1021/acsaem.2c03466) 2022 (early version)
 - 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  (early version)
 - (News & Views): A. Mannodi-Kanakkithodi [_Nature Physics_](https://doi.org/10.1038/s41567-023-02049-9) 2023 ([Free-to-read link](https://t.co/EetpnRgjzh))
 
+<!-- Wenzhen paper -->
 <!-- Se -->
 <!-- Oba book -->
 <!-- BiOI -->

diff --git a/docs/conf.py b/docs/conf.py
@@ -25,7 +25,7 @@
 author = 'Irea Mosquera-Lois, Seán R. Kavanagh'
 
 # The full version, including alpha/beta/rc tags
-release = '3.2.4'
+release = '3.3.0'
 
 
 # -- General configuration ---------------------------------------------------

diff --git a/docs/distortion_metadata.json b/docs/distortion_metadata.json
diff --git a/docs/index.rst b/docs/index.rst
@@ -211,6 +211,7 @@ run tests and add new tests for any new features whenever submitting pull reques
 Studies using ``ShakeNBreak``
 =============================
 
+- X\. Wang et al. `arXiv <https://arxiv.org/abs/2402.04434>`_ 2024
 - I\. Mosquera-Lois et al. `arXiv <https://doi.org/10.48550/arXiv.2401.12127>`_ 2024
 - K\. Li et al. `ChemRxiv <https://chemrxiv.org/engage/chemrxiv/article-details/65846b8366c1381729bc5f23>`_ 2024
 - X\. Wang et al. `Physical Review B <https://journals.aps.org/prb/abstract/10.1103/PhysRevB.108.134102>`_ 2023
@@ -222,12 +223,13 @@ Studies using ``ShakeNBreak``
 - 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
+- Y-S\. Choi et al. `ACS Appl. Energy Mater. <https://doi.org/10.1021/acsaem.2c03466>`__ 2022 (early version)
 - S\. R. Kavanagh, D. O. Scanlon, A. Walsh `ACS Energy Letters`_ 2021
 - C\. J. Krajewska et al. `Chemical Science`_ 2021  (early version)
 - (News & Views): A. Mannodi-Kanakkithodi `Nature Physics`_ 2023 (`Free-to-read link <https://t.co/EetpnRgjzh>`__)
 
 .. Se
-.. Xinwei, Wenzhen early 2024 papers
+.. Wenzhen paper
 .. Oba book
 .. BiOI
 .. Kumagai collab paper

diff --git a/docs/v_Cd_s0_0.svg → docs/v_Cd_0.svg b/docs/v_Cd_s0_0.svg → docs/v_Cd_0.svg
diff --git a/docs/v_Cd_s0_0_colorbar.svg → docs/v_Cd_0_colorbar.svg b/docs/v_Cd_s0_0_colorbar.svg → docs/v_Cd_0_colorbar.svg