sisl 0.16.1 Release Notes
*************************

Released on 2025-05-28.


New features
============

- Full I/O support for buffers and zip files

  Up to now, the support for buffers was limited to text buffers. Now,
  byte buffers are also supported, so one can read/write binary files
  and CDF files from/to buffers.

  This change also introduced support for zipfiles.

  **Example for buffers:**

  Writing a grid to a buffer:

  .. code-block:: python

      import sisl
      import io

      geometry = sisl.geom.graphene()
      grid = sisl.Grid((2, 2, 2), geometry=geometry)
      grid[:] = np.random.random(grid.shape)

      buffer = io.BytesIO()

      nc = sisl.io.gridncSileSiesta(buffer, mode="wb")
      nc.write_grid(grid)

  Reading a grid from a buffer:

  .. code-block:: python

      import sisl
      import io

      buffer = ... # Get a buffer with the grid data

      grid = sisl.io.gridncSileSiesta(buffer).read_grid()

  **Example for zip files:**

  Reading the Hamiltonian from a SIESTA run inside a zip file:

  .. code-block:: python

      import sisl

      sisl.get_sile("/path/to/data.zip/run/RUN.fdf").read_hamiltonian()

  Writing a Hamiltonian inside a zip file:

  ..  code-block:: python

      import sisl

      geom = sisl.geom.graphene()
      H = sisl.Hamiltonian(geom)

      H.write_hamiltonian("/path/to/data.zip/graphene.HSX")

  By passing the path inside the zip file as a string, ``sisl`` will
  automatically create the ``zipfile.ZipFile`` object and close it
  when it is done. If you don't want the zip file to be closed, you can
  create it externally and then pass a ``zipfile.Path`` to ``sisl``:

  .. code-block:: python

      import sisl
      import zipfile

      # Create a zip file or append to an existing one
      zip_file = zipfile.ZipFile("myzipfile.zip", "a")
      # Define path inside the zip file
      H_path = zipfile.Path(zip_file, "graphene.HSX")

      geom = sisl.geom.graphene()
      H = sisl.Hamiltonian(geom)

      H.write_hamiltonian(H_path)

      # Now the zip file is not closed, it is up to you to close it
      # when you are done
      zip_file.close()

  (:pull:`914`)


- Added `prune_range` to matrices

  This allows one to remove couplings
  that are further than some distance.
  It isn't fully implemented for atomic sub-sets.
  But should be implemented in the future.


- Added pressure and efield unit types


- Added rotation_matrix to make rotations simpler

  Also enabled `order` argument to `spin_rotate`.



Changes and improvements
========================

- Added and made CODATA-2022 values the default

  Now a wider range of CODATA values
  are available. One can switch between
  used version by using `SISL_CODATA=2018|2022`
  if needed.

  (:pull:`913`)


- Allow `spin_rotate`/`spin_align` on other than `DensityMatrix` objects

  This is needed because one might equally be interested in this
  for Hamiltonians etc.

  (:pull:`921`)



Bugfixes
========

- Allowed complex data-types in DensityMatrix methods

  In particular `spin_align`, `spin_rotate` and `mulliken`
  are now fixed for any data-type.

  (:pull:`911`)


- Fixed `stdoutSileSiesta.read_scf`

  It parsed the wrong spin moment and so
  had a wrong read of the first SCF iteration.

  (:pull:`919`)