zerothi · zerothi · Mar 19, 2024 · Feb 22, 2024 · Feb 23, 2024 · Mar 18, 2024
diff --git a/.binder/postBuild b/.binder/postBuild
@@ -8,4 +8,4 @@ env
 echo "### mybinder environment^^^"
 
 # Manually install the necessary stuff for sisl
-python3 -m pip install -vv Cython tqdm matplotlib xarray plotly .
+python3 -m pip install -vv tqdm matplotlib netCDF4 plotly .
diff --git a/.gitignore b/.gitignore
@@ -9,10 +9,9 @@ build
 *.c
 __config__.py
 
+.*/
 docs/build
 docs/**/generated/
-docs/sisl
-
 */sisl.egg-info
 src/sisl/**/*.html
 src/sisl/_version.py

diff --git a/docs/api/basic.rst b/docs/api/basic.rst
@@ -14,7 +14,7 @@ unit cells and grid functions.
 Simple objects
 ==============
 
-.. index:: basic, geometry, supercell, atom, atom, orbital
+.. index:: basic, geometry, lattice, supercell, atom, orbital
 
 .. autosummary::
    :toctree: generated/
@@ -66,6 +66,6 @@ In particular `oplist` is useful when calculating averages in Brillouin zones (s
 .. autosummary::
    :toctree: generated/
 
-   NeighborFinder
-   oplist
+   ~sisl.oplist
+   ~sisl.geom.NeighborFinder
    ~sisl.utils.PropertyDict
diff --git a/docs/api/core.rst b/docs/api/core.rst
@@ -1,8 +1,8 @@
 .. _core:
 
-**********
-Functional
-**********
+**********************
+Functional programming
+**********************
 
 .. currentmodule:: sisl
 

diff --git a/docs/api/default_geom.rst b/docs/api/default_geom.rst
@@ -12,7 +12,7 @@ A selection of default geometries that `sisl` can construct on the fly.
 While this is far from complete we encourage users to contribute additional
 geometries via a `pull request <pr>`_.
 
-All methods return a `Geometry` object.
+All methods returns a `Geometry` object.
 
 Some of the geometries are created in section based geometries, such as `heteroribbon`.
 This functionality is provided through the `composite_geometry`
@@ -27,9 +27,9 @@ Bulk
    sc
    bcc
    fcc
-   rocksalt
    hcp
    diamond
+   rocksalt
 
 
 Surfaces (slabs)
@@ -88,4 +88,3 @@ Helpers
    AtomCategory
    composite_geometry
    CompositeGeometrySection
-
diff --git a/docs/api/index.rst b/docs/api/index.rst
@@ -8,8 +8,8 @@ API documentation
 :Date: |today|
 
 
-.. module:: sisl
-       
+.. currentmodule:: sisl
+
 This reference manual describes in detail how the modules, classes
 and functions can be used and how their API's are defined.
 
@@ -28,11 +28,11 @@ All methods and submodules are listed  :ref:`here <genindex>` and
    viz/index
    unit_constant
    utilities
-   core
 
 .. toctree::
    :maxdepth: 1
 
+   core
    io/index
 
 .. toctree::

diff --git a/docs/api/physics.matrix.rst b/docs/api/physics.matrix.rst
@@ -50,7 +50,7 @@ out semi-infinite regions.
 Bloch's theorem
 ---------------
 
-Bloch's theorem is a very powerful proceduce that enables one to utilize
+Bloch's theorem is a very powerful procedure that enables one to utilize
 the periodicity of a given direction to describe the complete system.
 
 .. autosummary::

diff --git a/docs/changelog/index.rst b/docs/changelog/index.rst
@@ -8,8 +8,8 @@ scripts to the API changes.
 
 Generally this can be accommodated by using a code ``if`` block:
 
-.. code::
-   
+.. code-block::
+
     if sisl.__version_tuple__[:3] >= (0, 13, 0):
        pass
     else:
@@ -24,6 +24,9 @@ In any case the following list of release notes may be used to check changes
 between versions.
 
 
+Changelogs
+----------
+
 .. toctree::
    :maxdepth: 1
 
@@ -51,4 +54,3 @@ between versions.
    v0.8.2
    v0.8.1
    v0.8.0
-
diff --git a/docs/changelog/v0.14.0.rst b/docs/changelog/v0.14.0.rst
@@ -66,7 +66,7 @@ Added
      * "hello.xyz{contains=<name>}" equivalent to "hello.xyz{<name>}"
      * "hello.xyz{startswith=<name>}" class name should start with `<name>`
      * "hello.xyz{endswith=<name>}" class name should end with `<name>`
-        This is useful for defining a currently working code:
+       This is useful for defining a currently working code:
 
             SISL_IO_DEFAULT=siesta
 
@@ -85,10 +85,10 @@ Added
 * unified the index argument for reading Grids, `read_grid`, this influences
   Siesta and VASP grid reads.
 * `sisl.mixing`:
-  * `AndersonMixer` enables the popular and very simple linear-like mixer
-  * `StepMixer` allows switching between different mixers, for instance this
-    enabled restart capabilities among other things.
-  * Enabled composite mixers (simple math with mixers)
+   * `AndersonMixer` enables the popular and very simple linear-like mixer
+   * `StepMixer` allows switching between different mixers, for instance this
+      enabled restart capabilities among other things.
+   * Enabled composite mixers (simple math with mixers)
 * `BrillouinZone.merge` allows simple merging of several objects, #537
 
 Changed
@@ -156,7 +156,7 @@ Fixed
 
 
 toolbox.btd
-^^^^^^^^^^^^
-# Added
+-----------
+Added
 ^^^^^^^^
 * calculation of scattering matrices
diff --git a/docs/changelog/v0.14.2.rst b/docs/changelog/v0.14.2.rst
@@ -1,3 +1,6 @@
+******
+0.14.2
+******
 
 Released 4 of October 2023.
 

diff --git a/docs/changelog/v0.14.3.rst b/docs/changelog/v0.14.3.rst
@@ -1,3 +1,6 @@
+******
+0.14.3
+******
 
 Released 7 of November 2023.
 

diff --git a/docs/cite.rst b/docs/cite.rst
@@ -8,12 +8,13 @@ released under the MPL-2 license.
 
 You are encouraged to cite sisl when you use it to produce scientific contributions.
 
-The sisl citation can be found through Zenodo:
-
-|zenodo|_
+The sisl citation can be found through Zenodo: |zenodo|_
 
 By citing sisl you are encouraging development and exposing the software package.
 
+.. |zenodo| image:: https://zenodo.org/badge/doi/10.5281/zenodo.597181.svg
+.. _zenodo: https://doi.org/10.5281/zenodo.597181
+
 
 Citing basic usage
 ------------------
@@ -52,7 +53,7 @@ When using sisl as tight-binding setup for Hamiltonians and/or dynamical matrice
 `TBtrans`_ and/or ``PHtrans`` you should cite these two DOI's:
 
 
-.. code-block:: bash
+.. code-block:: console
 
     @software{zerothi_sisl,
       author       = {Papior, Nick},
@@ -76,6 +77,55 @@ When using sisl as tight-binding setup for Hamiltonians and/or dynamical matrice
     }
 
 
+If using real-space self-energies one should additionally cite:
 
-.. |zenodo| image:: https://zenodo.org/badge/doi/10.5281/zenodo.597181.svg
-.. _zenodo: https://doi.org/10.5281/zenodo.597181
+.. code-block:: console
+
+    @article{papior2019,
+       author = {Papior, Nick and Calogero, Gaetano and Leitherer, Susanne and Brandbyge, Mads},
+       doi = {10.1103/physrevb.100.195417},
+       number = {19},
+       source = {Crossref},
+       url = {https://doi.org/10.1103/physrevb.100.195417},
+       volume = {100},
+       journal = {Phys. Rev. B},
+       publisher = {American Physical Society (APS)},
+       title = {Removing all periodic boundary conditions: {Efficient} nonequilibrium Green's function calculations},
+       issn = {2469-9950, 2469-9969},
+       year = {2019},
+       month = nov,
+    }
+
+
+
+.. _publications:
+
+Publications using sisl
+-----------------------
+
+The `sisl` tool-suite has been used one way or the other in the listed
+publications below.
+
+Please help maintaining the list complete via a `pull request <pr_>`_ or
+by writing an email to `nickpapior AT gmail.com <mailto:nickpapior@gmail.com>`_.
+
+
+.. bibliography:: sisl_uses.bib
+   :list: enumerated
+   :all:
+   :style: rev_year
+   :labelprefix: U
+
+
+arXiv publications
+------------------
+
+These publications are as far as we know in the review process.
+
+- D. Weckbecker, M. Fleischmann, R. Gupta, W. Landgraf, S. Leitherer, O. Pankratov, S. Sharma, V. Meded, S. Shallcross,
+  *Moiré ordered current loops in the graphene twist bilayer*,
+  :doi:`1901.04712 <10.48550/arXiv.1901.04712>`
+
+- Y. Guan, O.V. Yazyev,
+  *Electronic transport in graphene with out-of-plane disorder*,
+  :doi:`2210.16629 <10.48550/arXiv.2210.16629>`
-Original file line number
+Diff line change
@@ -1,3 +1,6 @@
+    ******
+.14.2
+    ******
     Released 4 of October 2023.
@@ Expand Down @@