0.12.0

Released 28 of January 2022.

Contributors

A total of 4 people contributed to this release. People with a “+” by their names contributed a patch for the first time.

A total of 14 pull requests were merged for this release.

Geometry.sub_orbital is added
BrillouinZone.volume enables easy calculation of volumes for BZ integrals
State.sub|remove are now allowed to be done inplace
State.derivative can now correctly calculate 1st and 2nd order derivatives #406
Enabled discontinuity jumps in band-structures (pass points as None)
COOP and COHP calculations for eigenstates
inverse participation ration calculations (with arbitrary q)
origin point for mirror functionality (Geometry)
degenerate_dir for velocity directions
State.remove complementary to State.sub
copying Dispatchers for subclasses.
dispatchers to Shape
Spin.spinor to get number of spinor components
sc argument to xyzSile.read_geometry for user defined cells
tiling a State object, #354 and #355
replacing atoms in SparseOrbital geometries #139
direction now accepts abc and xyz keywords to retrieve vectors depending on direction input.
replacing atoms in SparseOrbital geometries #139
reading from STRUCT_* files (Siesta input/output) #308
reading the SuperCell block from fdf
reading PAO.Basis blocks from both out and fdf files, almost complete functionality #90
generic transform method for matrix transformations
doing ufunc.reduce on SparseCSR matrices; wrong values for e.g. np.prod, generally be CAUTIOUS with reduction operations
transposing a SparseCSR matrix
added pymatgen conversion (Geometry.to/new.pymatgen)
atom indexing by shapes #337

sub_orbital allows lists of orbitals
berry_phase now works for non-orthogonal basis sets (uses Lowdin transformation) This may require sufficiently small dk for accurateness.
degenerate argument for conductivity to enable decoupling of states
BandStructure.lineark now always starts from 0
reading coordinates from siesta.out when bands are calculated #362
complex warning for spin_moment #360 and #363
partially fixed #102 (wavefunction for fxyz outside box, related to #365 and how origin is interpreted in the code
non-collinear PDOS plotting
improvement for BandStructure setup, arguments more stringent
several fixes for sisl.viz; #368, #376 and #382
empty array handlings in _sanitize_* #370
ensured AtomicOrbital can be instantiated without specifying m (default to 0)
fixed bug when copying orbitals
fixed reading atomic labels in xsf files #402
fixed hpc parameters #403

order of arguments for nanoribbon it was not consistent with the others
removed cell argument in Geometry.sub
removed Sile.exist, refer to Sile.file which always will be a pathlib.Path instance
berry_phase now uses the gauge=R convention, the code became much simpler
BrillouinZone.parametrize function changed interface to allow more dimensions
EigenStateElectron.inner does not use the overlap matrix by default, norm2 is for exactly this behaviour
changed license to MPLv2 makes toolboxes easier to contribute under different license
renamed origo to origin, see #365
default parallel calculations are disabled
changed State.align_* routines to align self rather than other
doc fixes for recommending python -m pip