v0.12.0
Contributors
A total of 4 people contributed to this release. People with a "+" by their
names contributed a patch for the first time.
- A.H. Kole +
- Nick Papior
- Pol Febrer
- Thomas Frederiksen
Pull requests merged
A total of 14 pull requests were merged for this release.
- #307 : Reading net charges from outSileSiesta
- #313 : doc: added description of dictionary keys and fixed a typo
- #365 : mnt: changed all origo references to origin
- #367 : Parallel calculation of PDOS and (fat)bands
- #368 : Allow per-category atom styles in GeometryPlot
- #371 : bug: fixed some errors in tutorial notebooks
- #374 : bug: geometry plot tests were failing
- #376 : tests: removed plotly requirement to test sisl.viz
- #378 : mnt: fixed matplotlib tests in <=3.4
- #382 : bug: 2D geometry plots didn't take perspective into account.
- #395 : Quick bug fix. Plot was not callable.
- #397 : tests: avoid too many matplotlib figures
- #402 : Use PeriodicTable to convert atomic labels to atomic numbers...
- #403 : Fixed construction of non-orthogonal (2-atom) hcp cell
Added
- 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 toState.sub
- copying Dispatchers for subclasses.
- dispatchers to
Shape
Spin.spinor
to get number of spinor componentssc
argument toxyzSile.read_geometry
for user defined cells- tiling a State object, #354 and #355
- replacing atoms in SparseOrbital geometries #139
- direction now accepts
abc
andxyz
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/from.pymatgen)
- atom indexing by shapes #337
Fixed
sub_orbital
allows lists of orbitalsberry_phase
now works for non-orthogonal basis sets (uses Lowdin transformation)
This may require sufficiently small dk for accurateness.degenerate
argument forconductivity
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
forfxyz
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
Changed
- order of arguments for
nanoribbon
it was not consistent with the others - removed cell argument in
Geometry.sub
- removed
Sile.exist
, refer toSile.file
which always will be apathlib.Path
instance berry_phase
now uses the gauge=R convention, the code became much simplerBrillouinZone.parametrize
function changed interface to allow more dimensionsEigenStateElectron.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 alignself
rather thanother
- doc fixes for recommending
python -m pip
Removed
- removed keywords align for State.inner|outer, manually use
align
if required - removed method
State.expectation
toolbox.btd
Added
- calculation of scattering states and eigenchannels
- multiple variants of scattering state methods