Merge pull request #34 from SMTG-UCL/develop

Merging as tests have passed

CHANGELOG.rst

@@ -1,6 +1,23 @@
 Change Log
 ==========
 
+v22.11.17
+--------
+
+Main changes:
+
+- Refactor :code:`Distortions()` to a list or simple-format dict of :code:`Defect` objects as input.
+  Same for :code:`Distortions.from_structures()`
+- Update defect naming to :code:`{Defect.name}_s{Defect.defect_site_index}` for vacancies/substitutions and
+  :code:`{Defect.name}_m{Defect.multiplicity}` for interstitials. Append "a", "b", "c" etc in cases of inequivalent
+  defects
+- Make :code:`ShakeNBreak` compatible with most recent :code:`pymatgen` and :code:`pymatgen-analysis-defects` packages.
+- Update legend format in plots and site index/multiplicity labelling, make default format png.
+- Update default charge state setting to match :code:`pymatgen-analysis-defects` oxi state + padding approach.
+- A lot of additional warning and error catches.
+- Miscellaneous warnings and docs updates.
+
+
 v22.11.7
 --------
 

README.md

@@ -35,6 +35,8 @@ If using `VASP`, in order for `ShakeNBreak` to automatically generate the pseudo
 ```
    Within your `VASP` pseudopotential top directory, you should have a folder named `POT_GGA_PAW_PBE` which contains the `POTCAR.X(.gz)` files (in this case for PBE `POTCAR`s). More details given [here](https://pymatgen.org/installation.html#potcar-setup).
 
+The font Montserrat ([Open Font License](https://scripts.sil.org/cms/scripts/page.php?site_id=nrsi&id=OFL)) will be installed with the package, and will be used by default for plotting.
+
 ### Developer installation
 For development work, ShakeNBreak can also be installed from a copy of the source directory:
 
@@ -77,12 +79,19 @@ More information about each function and its inputs/outputs are available from t
 We recommend at least looking through the [tutorials](https://shakenbreak.readthedocs.io/en/latest/Tutorials.html) when first starting to use `ShakeNBreak`, to familiarise yourself with the full functionality and workflow.
 
 ## Code Compatibility
-`ShakeNBreak` is built to natively function using `pymatgen` `Defect` objects ([docs available here](https://materialsproject.github.io/pymatgen-analysis-defects/)) and be compatible with the most recent version of `pymatgen`. If you are receiving `pymatgen`-related errors when using `ShakeNBreak`, you may need to update `pymatgen` and/or `ShakeNBreak`, which can be done with:
+`ShakeNBreak` is built to natively function using `pymatgen` `Defect` objects ([docs available here](https://materialsproject.github.io/pymatgen-analysis-defects/)) and be compatible with the most recent version of `pymatgen`.
+If you are receiving `pymatgen`-related errors when using `ShakeNBreak`, you may need to update `pymatgen` and/or `ShakeNBreak`, which can be done with:
 ```bash
 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` defect dictionaries or structure files (e.g. `POSCAR`s for `VASP`) as inputs. As such, it should be compatible with any defect code (such as `doped`, `DASP`, `PyLada`, `PyCDT`, `Spinney`, `DefAP`, `PyDEF`, `pydefect`...) that generates these files.
+`ShakeNBreak` can take `pymatgen` `Defect` objects as input (to then generate the trial distorted structures),
+**_but also_** can take in `pymatgen` `Structure` objects, `doped` defect dictionaries 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://github.com/SMTG-UCL/doped), [`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.
 Please let us know if you have any issues with compatibility, or if you would like to see any additional features added to `ShakeNBreak` to make it more compatible with your code.
 
 ## Contributing

docs/Analysis.rst

@@ -18,7 +18,7 @@ Alternatively, we can run from a different directory and specify the defect to p
 
 .. code:: bash
 
-    $ snb-parse --defect vac_1_Cd_0 --path defects_folder --code FHI-aims
+    $ snb-parse --defect v_Cd_s0_0 --path defects_folder --code FHI-aims
 
 Where ``defects_folder`` is the path to the top level directory containing the defect folder, and is only required if
 different from the current directory.
@@ -32,7 +32,7 @@ in a given/current directory using the ``-a``/``--all`` flag:
 
 This generates a ``yaml`` file for each defect, mapping each distortion to the
 final energy of the relaxed structures (in eV). These files are saved to the
-corresponding defect directory (e.g. ``defects_folder/vac_1_Cd_0/vac_1_Cd_0.yaml``).
+corresponding defect directory (e.g. ``defects_folder/v_Cd_s0_0/v_Cd_s0_0.yaml``).
 
 .. code:: yaml
 
@@ -61,7 +61,7 @@ was used (if not :code:`VASP`) and which reference structure to use (default = `
 
 .. code:: bash
 
-    $ snb-analyse --defect vac_1_Cd_0 --code FHI-aims --path defects_folder --ref_struct -0.4 --verbose
+    $ snb-analyse --defect v_Cd_s0_0 --code FHI-aims --path defects_folder --ref_struct -0.4 --verbose
 
 Again if we want to analyse the results for **all** defects present in a given/current directory, we can use the
 ``-a``/``--all`` flag:
@@ -90,7 +90,7 @@ the defect directory:
 
 which will generate a figure like the one below:
 
-.. image:: ./vac_1_Cd_0.svg
+.. image:: ./v_Cd_s0_0.svg
     :width: 400px
 
 ..
@@ -103,7 +103,7 @@ structures, using the ``-cb``/``--colorbar`` flag:
 
     $ snb-plot -cb
 
-.. image:: ./vac_1_Cd_0_colorbar.svg
+.. image:: ./v_Cd_s0_0_colorbar.svg
     :width: 450px
 
 ..
@@ -114,7 +114,7 @@ was used (if not :code:`VASP`) and other options (what ``metric`` to use for col
 
 .. code:: bash
 
-    $ snb-plot --defect vac_1_Cd_0 --code FHI-aims --path defects_folder --colorbar -0.4 --metric disp --units meV --verbose
+    $ snb-plot --defect v_Cd_s0_0 --code FHI-aims --path defects_folder --colorbar -0.4 --metric disp --units meV --verbose
 
 Again if we want to plot the results for **all** defects present in a given/current directory, we can use the
 ``-a``/``--all`` flag:
@@ -143,15 +143,15 @@ For example, if we have the following directory structure
 .. code:: bash
 
     ./
-    |--- vac_1_Cd_0/ <-- Neutral Cd vacancy
+    |--- v_Cd_s0_0/ <-- Neutral Cd vacancy
     |       |--- Unperturbed
     |       |
     |       |--- Bond_Distortion_-30.0% <-- Favourable distortion
     |       |
     |       |--- Bond_Distortion_30.0%
     |       | ...
     |
-    |--- vac_1_Cd_-1/ <-- Negatively charged Cd vacancy
+    |--- v_Cd_s0_-1/ <-- Negatively charged Cd vacancy
             |--- Unperturbed
             | ...
             |--- Bond_Distortion_50% <-- Favourable distortion
@@ -171,7 +171,7 @@ for the code specified with the flag ``--code`` (default = :code:`VASP`).
 .. code:: bash
 
     ./
-    |--- vac_1_Cd_0/
+    |--- v_Cd_s0_0/
     |       |--- Unperturbed
     |       |
     |       |--- Bond_Distortion_-30.0% <-- Favourable distortion
@@ -180,7 +180,7 @@ for the code specified with the flag ``--code`` (default = :code:`VASP`).
     |       | ...
     |       |--- Bond_Distortion_50.0%_from_-1 <-- Distortion from the -1 charge state
     |
-    |--- vac_1_Cd_-1/
+    |--- v_Cd_s0_-1/
             |--- Unperturbed
             | ...
             |--- Bond_Distortion_50% <-- Favourable distortion
@@ -214,7 +214,7 @@ This command will generate a ``Groundstate`` directory within each defect folder
 .. code:: bash
 
     ./
-    |--- vac_1_Cd_0/
+    |--- v_Cd_s0_0/
     |       |--- Unperturbed
     |       |
     |       |--- Bond_Distortion_-30.0%
@@ -224,7 +224,7 @@ This command will generate a ``Groundstate`` directory within each defect folder
     |       |--- Groundstate
     |               |--- POSCAR <-- Ground state structure
     |
-    |--- vac_1_Cd_-1/
+    |--- v_Cd_s0_-1/
             |--- Unperturbed
             | ...
             |--- Bond_Distortion_50%

docs/Code_Compatibility.rst

@@ -1,12 +1,23 @@
 Code Compatibility
 ========================
 
-:code:`ShakeNBreak` is built to natively function using :code:`pymatgen` :code:`Defect` objects (`docs available here <https://materialsproject.github.io/pymatgen-analysis-defects/>`_) and be compatible with the most recent version of :code:`pymatgen`. If you are receiving :code:`pymatgen`-related errors when using :code:`ShakeNBreak`, you may need to update :code:`pymatgen` and/or :code:`ShakeNBreak`, which can be done with:
+:code:`ShakeNBreak` is built to natively function using :code:`pymatgen` :code:`Defect` objects
+(`docs available here <https://materialsproject.github.io/pymatgen-analysis-defects/>`_) and be compatible with the
+most recent version of :code:`pymatgen`. If you are receiving :code:`pymatgen`-related errors when using
+:code:`ShakeNBreak`, you may need to update :code:`pymatgen` and/or :code:`ShakeNBreak`, which can be done with:
 
 .. code:: bash
 
    pip install --upgrade pymatgen shakenbreak
 
 
-: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 :code:`doped`, :code:`DASP`, :code:`PyLada`, :code:`PyCDT`, :code:`Spinney`, :code:`DefAP`, :code:`PyDEF`, :code:`pydefect`...) that generates these files.
-Please let us know if you have any issues with compatibility, or if you would like to see any additional features added to :code:`ShakeNBreak` to make it more compatible with your code.
+: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://github.com/SMTG-UCL/doped>`_, `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.
+
+Please let us know if you have any issues with compatibility, or if you would like to see any additional features added
+to :code:`ShakeNBreak` to make it more compatible with your code.

docs/Installation.rst

@@ -19,6 +19,12 @@ Within your ``VASP`` pseudopotential top directory, you should have a folder nam
 which contains the ``POTCAR.X(.gz)`` files (in this case for PBE ``POTCARs``). More details given
 `here <https://pymatgen.org/installation.html#potcar-setup>`_.
 
+.. NOTE::
+   The font `Montserrat <https://fonts.google.com/specimen/Montserrat/about>`
+   (`Open Font License <https://scripts.sil.org/cms/scripts/page.php?site_id=nrsi&id=OFL>`_)
+   will be installed with the package, and will be used by default for plotting. If you prefer to use a different
+   font, you can change the font in the ``matplotlib`` style sheet (in ``shakenbreak/shakenbreak.mplstyle``).
+
 Developer's installation (*optional*)
 -----------------------------------------