0.13.0

Released 18 of January 2023.

Contributors

A total of 5 people contributed to this release. People with a “+” by their names contributed a patch for the first time.

  • A.H. Kole

  • Nick Papior

  • Nils Wittemeier +

  • Pol Febrer

  • Thomas Frederiksen

Pull requests merged

A total of 18 pull requests were merged for this release.

  • #487: Fix issue 486 - in correct sign of the y component of the spin…

  • #489: bug: fixed #488 with the cell order

  • #494: enh: enabling reading of file-handles and StringIO

  • #498: 495 deprecation

  • #499: Easy construction of hydrogenic orbitals

  • #500: Reading output from ORCA

  • #503: Plotly is incompatible with ipywidgets 8.x

  • #504: Allow reading forces from transiesta in output file

  • #508: New keywords in step_to()

  • #510: Add CodeQL workflow for GitHub code scanning

  • #511: Possible bug: within_inf with periodic=False returns sc atoms…

  • #514: Surface slab geometries: clarify vacuum=None as a possibility…

  • #515: doc: fixed indices in sums

  • #516: mnt: changed index ordering of spin-charge quantities

  • #519: Fix reading of basis

  • #520: ORCA API

  • #521: Minor fixes for IO-API

  • #526: bug: reading the EDM from fdf did not read geometry automatically

Added

  • Geometry.apply apply functions to slices of data depending on the geometry

  • enabled Gaussian and Slater type orbitals, #463 Please give feedback!

  • deltancSileTBtrans.merge allowing easy merging of several delta siles, #513

  • implemented reading of output files from ORCA, #500

  • HydrogenicOrbital is added for simple handling of 1-valence electron orbitals, #499

  • Bohr radius to constants

  • enabled ASCII siles to read from file-handles and buffers, #484

  • enabled unit specification for lengths in cube-files

  • added kwargs passed to eigenstate functions in berry_phase and conductivity

  • ensured that non-orthogonal transform will copy over overlap matrix in case the matrix is only touching the non-overlap elements

  • enabled dictionary entries for the Atoms initialization in place of atoms argument. Both in the list-like entry, or as the only argument.

Fixed

  • rare compiler bug, #512

  • within_inf with periodic arguments, #511

  • reading TranSiesta data from outSileSiesta

  • regression from 80f27b05, reading version 0 HSX content, #492

  • delta-files (netCDF) would always have diagonal components, this has now been removed since it only needs the elements with values

  • Siesta sparse matrices could in some cases set wrong diagonal components

  • too large energies in Siesta files could result in crash, #482

  • orbital quantum numbers from HSX file was wrong in v1, #462

  • corrected sign for spin-Y direction, PDOS, spin_moment, #486

  • RealSpaceSI for right semi-infinite directions, #475

  • tbtrans files now have a separate entry in the documentation

Changed

  • removed all deprecated routines, #495

  • oplist now can do in-place operations on generators

  • significant performance improvement for COOP calculations, thanks to Susanne Leitherer for discovering the issue

  • changed argument order of ElectronState.COP

  • index ordering of spin and coordinate quantities are now changed to have these as the first indices. This ensures consistency across return types and allows easier handling. Note that non-polarized PDOS calculations now has an extra dimension for coherence with non-colinear spin. (see #501)

  • ensured all units are now CODATA-2018 values

  • cell_length changed to cell2length with new axes argument

  • enabled orbitals up to the h-shell, #491

  • swapped order of honeycomb (graphene derivatives) lattice vectors, to ensure the vectors are following right-hand-rule, #488

  • changed DIIS solver to assume the matrix is symmetric (it is)

  • tbtncSileTBtrans and its derivates has changed, drastically. This will accommodate changes related to #477 and #478. Now *_transmission refers to energy resolved transmissions and *_current reflects bias-window integrated quantities. The defaults and argument order has changed drastically, so users should adapt their scripts depending on sisl version. A check can be made, if sisl.__version_tuple__[:3] >= (0, 13, 0):

  • To streamline argument order the *_ACO[OH]P routines have changed elec and E argument order. This makes them compatible with orbital_transmission etc.