Merge pull request #77 from SMTG-Bham/develop

Develop

.github/workflows/lint.yml

@@ -37,7 +37,7 @@ jobs:
       - name: ruff
         run:  |
           ruff --version
-          ruff --fix shakenbreak
+          ruff check --fix shakenbreak
 
       - name: check docstrings
         run:  |
@@ -53,4 +53,4 @@ jobs:
       - name: flake8
         run:  |
           flake8 --version
-          flake8 --max-line-length 107 --color always --ignore=E121,E123,E126,E203,E226,E24,E704,W503,W504,F401,E203 shakenbreak
+          flake8 --max-line-length 107 --color always --ignore=E121,E123,E126,E203,E226,E24,E704,W503,W504,F401,E203 shakenbreak

CHANGELOG.rst

@@ -1,6 +1,11 @@
 Change Log
 ==========
 
+v3.3.6
+----------
+- Add `py.typed` to properly detect type hints by @Andrew-S-Rosen
+- `snb-run` updates to improve efficiency
+
 v3.3.5
 ----------
 - Enforce ``doped>=2.4.4`` requirement.

README.md

@@ -102,7 +102,7 @@ pip install --upgrade pymatgen shakenbreak
 `ShakeNBreak` can take `pymatgen` `Defect` objects as input (to then generate the trial distorted structures),
 **_but also_** can take in `pymatgen` `Structure` objects, `doped` defects or structure files
 (e.g. `POSCAR`s for `VASP`) as inputs. As such, it should be compatible with any defect code
-(such as [`doped`](https://doped.readthedocs.io/en/latest/index.html), [`pydefect`](https://github.com/kumagai-group/pydefect),
+(such as [`doped`](https://doped.readthedocs.io), [`pydefect`](https://github.com/kumagai-group/pydefect),
 [`PyCDT`](https://github.com/mbkumar/pycdt), [`PyLada`](https://github.com/pylada/pylada-defects),
 [`DASP`](http://hzwtech.com/files/software/DASP/htmlEnglish/index.html), [`Spinney`](https://gitlab.com/Marrigoni/spinney/-/tree/master),
 [`DefAP`](https://github.com/DefAP/defap), [`PyDEF`](https://github.com/PyDEF2/PyDEF-2.0)...) that generates these files.
@@ -128,10 +128,15 @@ Automatic testing is run on the master and develop branches using Github Actions
 
 ## Studies using `ShakeNBreak`
 
+- 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
+- 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
+- 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
 - X. Wang et al. **_Upper efficiency limit of Sb<sub>2</sub>Se<sub>3</sub> solar cells_** [_Joule_](https://doi.org/10.1016/j.joule.2024.05.004) 2024
-- I. Mosquera-Lois et al. **_Machine-learning structural reconstructions for accelerated point defect calculations_** [_arXiv_](https://doi.org/10.48550/arXiv.2401.12127) 2024
+- I. Mosquera-Lois et al. **_Machine-learning structural reconstructions for accelerated point defect calculations_** [_npj Computational Materials_](https://doi.org/10.1038/s41524-024-01303-9) 2024
 - S. R. Kavanagh et al. **_doped: Python toolkit for robust and repeatable charged defect supercell calculations_** [_Journal of Open Source Software_](https://doi.org/10.21105/joss.06433) 2024
 - K. Li et al. **_Computational Prediction of an Antimony-based n-type Transparent Conducting Oxide: F-doped Sb<sub>2</sub>O<sub>5</sub>_** [_Chemistry of Materials_](https://doi.org/10.1021/acs.chemmater.3c03257) 2024
 - X. Wang et al. **_Four-electron negative-U vacancy defects in antimony selenide_** [_Physical Review B_](https://journals.aps.org/prb/abstract/10.1103/PhysRevB.108.134102) 2023

docs/Analysis.rst

@@ -248,11 +248,11 @@ Further Defect Analysis
 -------------------------
 Once the ground state (and metastable) defect structures have been identified, we will want to compute
 their formation energies using our final fully-converged calculation parameters (i.e. plane-wave cutoff
-and k-point sampling). This can be done using `doped <https://doped.readthedocs.io/en/latest/index.html>`_,
+and k-point sampling). This can be done using `doped <https://doped.readthedocs.io>`_,
 manually (not recommended) or using the other defect codes listed on the
 `Code Compatibility <https://shakenbreak.readthedocs.io/en/latest/Code_Compatibility.html>`_ page.
 
-As shown in the `doped <https://doped.readthedocs.io/en/latest/index.html>`_ tutorials and docs, you may
+As shown in the `doped <https://doped.readthedocs.io>`_ tutorials and docs, you may
 want to further analyse the behaviour and impact on material properties of your defects using advanced
 defect analysis codes such as `easyunfold <https://smtg-bham.github.io/easyunfold/>`_ (to analyse the
 electronic structure of defects in your material),

docs/Code_Compatibility.rst

@@ -14,7 +14,7 @@ most recent version of :code:`pymatgen`. If you are receiving :code:`pymatgen`-r
 :code:`ShakeNBreak` can take :code:`pymatgen` :code:`DefectEntry` objects as input (to then generate the trial distorted
 structures), **but also** can take in :code:`pymatgen` :code:`Structure` objects, :code:`doped` defect dictionaries or
 structure files (e.g. :code:`POSCAR`\s for :code:`VASP`) as inputs. As such, it should be compatible with any defect code
-(such as `doped <https://doped.readthedocs.io/en/latest/index.html>`_, `pydefect <https://github.com/kumagai-group/pydefect>`_,
+(such as `doped <https://doped.readthedocs.io>`_, `pydefect <https://github.com/kumagai-group/pydefect>`_,
 `PyCDT <https://github.com/mbkumar/pycdt>`_, `PyLada <https://github.com/pylada/pylada-defects>`_,
 `DASP <http://hzwtech.com/files/software/DASP/htmlEnglish/index.html>`_, `Spinney <https://gitlab.com/Marrigoni/spinney/-/tree/master>`_,
 `DefAP <https://github.com/DefAP/defap>`_, `PyDEF <https://github.com/PyDEF2/PyDEF-2.0>`_...) that generates these files.

docs/ShakeNBreak_Example_Workflow.ipynb

@@ -130,7 +130,7 @@
    "id": "9a98b5d2-c17f-4d00-8a0f-b5dfe8997420",
    "metadata": {},
    "source": [
-    "## 1. Generate defects with [`doped`](https://doped.readthedocs.io/en/latest/)/`pymatgen`"
+    "## 1. Generate defects with [`doped`](https://doped.readthedocs.io)/`pymatgen`"
    ]
   },
   {
@@ -139,9 +139,9 @@
    "metadata": {},
    "source": [
     "The input defect objects for `ShakeNBreak` can be generated using either\n",
-    "[`doped`](https://doped.readthedocs.io/en/latest/), `pymatgen` or alternatively just\n",
+    "[`doped`](https://doped.readthedocs.io), `pymatgen` or alternatively just\n",
     " the bulk and defect structures can be provided. Below we show how to generate the defect `python`\n",
-    " objects using [`doped`](https://doped.readthedocs.io/en/latest/) (Section\n",
+    " objects using [`doped`](https://doped.readthedocs.io) (Section\n",
     " 1.1) and `pymatgen` (Section 1.1).\n",
     "\n",
     "In this case we take CdTe as our example system:"
@@ -163,7 +163,7 @@
    "metadata": {},
    "source": [
     "To generate defects with doped, we can use the code below. This procedure is described in much more\n",
-    "detail on the [`doped` docs](https://doped.readthedocs.io/en/latest/), which also shows how to generate\n",
+    "detail on the [`doped` docs](https://doped.readthedocs.io), which also shows how to generate\n",
     "and calculate the chemical potential terms (needed for defect formation energies), perform defect\n",
     "supercell (finite-size) charge\n",
     " corrections, calculate & plot the final defect formation energy diagram, and perform further defect\n",
@@ -960,7 +960,7 @@
        "        folder names will be set equal to `DefectEntry.name` if the `name`\n",
        "        attribute is set for all input `DefectEntry`s, otherwise generated\n",
        "        according to the `doped` convention\n",
-       "        (see: https://doped.readthedocs.io/en/latest/dope_workflow_example.html).\n",
+       "        (see: https://doped.readthedocs.io/en/latest/generation_tutorial.html).\n",
        "\n",
        "        Defect charge states (from which bond distortions are determined) are\n",
        "        taken from the `DefectEntry.charge_state` property.\n",
@@ -3946,9 +3946,9 @@
    "metadata": {},
    "source": [
     "### Further Defect Analysis\n",
-    "Once the ground state (and metastable) defect structures have been identified, we will want to compute their formation energies using our final fully-converged calculation parameters (i.e. plane-wave cutoff and k-point sampling). This can be done using [`doped`](https://doped.readthedocs.io/en/latest/), manually (not recommended) or using the other defect codes listed on the [Code Compatibility](https://shakenbreak.readthedocs.io/en/latest/Code_Compatibility.html) page.\n",
+    "Once the ground state (and metastable) defect structures have been identified, we will want to compute their formation energies using our final fully-converged calculation parameters (i.e. plane-wave cutoff and k-point sampling). This can be done using [`doped`](https://doped.readthedocs.io), manually (not recommended) or using the other defect codes listed on the [Code Compatibility](https://shakenbreak.readthedocs.io/en/latest/Code_Compatibility.html) page.\n",
     "\n",
-    "As shown in the [`doped`](https://doped.readthedocs.io/en/latest/) examples and docs, you may want to further analyse the behaviour and impact on material properties of your defects using advanced defect analysis codes such as [`easyunfold`](https://smtg-bham.github.io/easyunfold/) (to analyse the electronic structure of defects in your material), [`py-sc-fermi`](https://py-sc-fermi.readthedocs.io/en/latest/) (to analyse defect concentrations, doping and Fermi level tuning), or [`nonrad`](https://nonrad.readthedocs.io/en/latest/)/[`CarrierCapture.jl`](https://wmd-group.github.io/CarrierCapture.jl/dev/) (to analyse non-radiative electron-hole recombination at defects)."
+    "As shown in the [`doped`](https://doped.readthedocs.io) examples and docs, you may want to further analyse the behaviour and impact on material properties of your defects using advanced defect analysis codes such as [`easyunfold`](https://smtg-bham.github.io/easyunfold/) (to analyse the electronic structure of defects in your material), [`py-sc-fermi`](https://py-sc-fermi.readthedocs.io/en/latest/) (to analyse defect concentrations, doping and Fermi level tuning), or [`nonrad`](https://nonrad.readthedocs.io/en/latest/)/[`CarrierCapture.jl`](https://wmd-group.github.io/CarrierCapture.jl/dev/) (to analyse non-radiative electron-hole recombination at defects)."
    ]
   },
   {

docs/Tips.rst

@@ -220,7 +220,7 @@ message about the origin of the problem, it is likely to be an issue with your v
 
 If this does not solve your issue, please check the specific cases noted below. If your issue still isn't
 solved, then please contact the developers through the ``GitHub``
-`Issues <https://github.com/SMTG-Bham/ShakeNBreak/issues>`_ page, or by email.
+`Issues <https://github.com/SMTG-Bham/ShakeNBreak/issues>`_ page.
 
 - A current known issue with ``numpy``/``pymatgen`` is that it might give an error similar to this:
 

docs/conf.py

@@ -25,7 +25,7 @@
 author = 'Irea Mosquera-Lois, Seán R. Kavanagh'
 
 # The full version, including alpha/beta/rc tags
-release = '3.3.5'
+release = '3.3.6'
 
 
 # -- General configuration ---------------------------------------------------

docs/index.rst

@@ -171,7 +171,7 @@ Code Compatibility
 :code:`ShakeNBreak` can take :code:`pymatgen` :code:`Defect` objects as input (to then generate the trial distorted
 structures), **but also** can take in :code:`pymatgen` :code:`Structure` objects, :code:`doped` defect dictionaries or
 structure files (e.g. :code:`POSCAR`\s for :code:`VASP`) as inputs. As such, it should be compatible with any defect code
-(such as `doped <https://doped.readthedocs.io/en/latest/index.html>`_, `pydefect <https://github.com/kumagai-group/pydefect>`_,
+(such as `doped <https://doped.readthedocs.io>`_, `pydefect <https://github.com/kumagai-group/pydefect>`_,
 `PyCDT <https://github.com/mbkumar/pycdt>`_, `PyLada <https://github.com/pylada/pylada-defects>`_,
 `DASP <http://hzwtech.com/files/software/DASP/htmlEnglish/index.html>`_, `Spinney <https://gitlab.com/Marrigoni/spinney/-/tree/master>`_,
 `DefAP <https://github.com/DefAP/defap>`_, `PyDEF <https://github.com/PyDEF2/PyDEF-2.0>`_...) that generates these files.
@@ -211,10 +211,14 @@ run tests and add new tests for any new features whenever submitting pull reques
 Studies using ``ShakeNBreak``
 =============================
 
+- 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
 - X\. Wang et al. **Upper efficiency limit of Sb₂Se₃ solar cells** `Joule <https://doi.org/10.1016/j.joule.2024.05.004>`_ 2024
-- I\. Mosquera-Lois et al. **Machine-learning structural reconstructions for accelerated point defect calculations** `arXiv <https://doi.org/10.48550/arXiv.2401.12127>`_ 2024
+- I\. Mosquera-Lois et al. **Machine-learning structural reconstructions for accelerated point defect calculations** `npj Computational Materials <https://doi.org/10.1038/s41524-024-01303-9>`_ 2024
 - S\. R. Kavanagh et al. **doped: Python toolkit for robust and repeatable charged defect supercell calculations** `Journal of Open Source Software <https://doi.org/10.21105/joss.06433>`_ 2024
 - K\. Li et al. **Computational Prediction of an Antimony-based n-type Transparent Conducting Oxide: F-doped Sb₂O₅** `Chemistry of Materials <https://doi.org/10.1021/acs.chemmater.3c03257>`_ 2024
 - X\. Wang et al. **Four-electron negative-U vacancy defects in antimony selenide** `Physical Review B <https://journals.aps.org/prb/abstract/10.1103/PhysRevB.108.134102>`_ 2023

setup.py

@@ -131,7 +131,7 @@ def package_files(directory):
 
 setup(
     name="shakenbreak",
-    version="3.3.5",
+    version="3.3.6",
     description="Package to generate and analyse distorted defect structures, in order to "
     "identify ground-state and metastable defect configurations.",
     long_description=long_description,