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 total of 18 pull requests were merged for this release.

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.

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

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.