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.