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:

  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:

  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:

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

  Writing a Hamiltonian inside a zip file:

  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:

  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()
  

  (PR914)

• 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.

  (PR913)

• Allow spin_rotate/spin_align on other than DensityMatrix objects

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

  (PR921)

Bugfixes

• Allowed complex data-types in DensityMatrix methods

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

  (PR911)

• Fixed stdoutSileSiesta.read_scf

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

  (PR919)