Sisl

Added
- enabled parsing geometry.in files from FHIaims
- added `batched_indices` for memory-reduced location of array values
- enabled manifold extractions `sisl.physics.yield_manifolds`
- enabled center of mass for periodic systems (chooses *best* COM)
- enabled returning the overlap matrix from `berry_phase`
- added `rocksalt` tfrederiksen
- slab geometry creations, `fcc_slab`, `bcc_slab` and `rocksalt_slab` tfrederiksen
- added `Geometry.translate2uc` to shift everything into the unit-cell tfrederiksen
- added `Geometry.unrepeat` to reverse `repeat` calls (and to `sgeom`)
- added `SparseGeometry.unrepeat` to reverse `repeat` calls

Fixed
- enabled reading HSX file version 1, 432
- major performance boost for reading GULP FC files
- cleaned mixing methods and decoupled the History and Mixers
- incorrect handling of `atoms` argument in `Geometry.center` calls

Changed
- State*.outer corrected to the same interface as State*.inner
- all `sisl.geom` geometries are now calling `optimize_nsc` if needed
- `SparseGeometry.cut` -> `SparseGeometry.untile`
- much faster
- many more checks to warn about wrong usage
- `cut` is now deprecated (removed in 0.13)
- changed the --cut flag in `sgeom` to `--untile`, deprecated flag
- enabled in/out arguments to tbt siles (easier to remember meaning)

Added
- return spin moment from SCF output files of Siesta
- read_fermi_level to siesta.PDOS files

Fixed
- MacOS builds
- `sdata` handling of siesta.PDOS* files, much more versatily now
- masking import of xarray
- Fixes to sisl.viz module related to 3.10 and other details

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 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

Fixed
- `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

Changed
- 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`

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

- **Major addition**: plotly backend for plotting and interaction with
output. This is still a work in progress made by Pol Febrer.
Many thanks to pfebrer!

- Added unzip argument to BZ.apply methods to unzip multiple
return values, also added documentation to reflect this

- Fixed reading data-arrays from Siesta-PDOS files

- Enabled minimization method for basis information and pseudo generation

- Enabled plotting grids using the command-line

- Bug in how non-colinear matrices are dealt with, now fixed
Thanks to Xe Hu for discovering this.

- Allowed reading the geometry for supercell HSX files
Atomic coordinates and nsc are determined from xij arrays

- Basic implementation of Hermitian construct.
It now ensures a correct Hermitian matrix for simple cases

- Added more return from close/within, supercell offsets
may be queried (ret_isc)

- Added more transposing functionality for spin matrices

- Fixed wfsxSileSiesta returning proper k-points if a geometry
is passed (i.e. reduced k-points). Otherwise warns users

- Huge performance increase for finalizing very large structures

- Fixed writing %block in fdf files

- Enabled reading Fermi level from VASP DOSCAR files

- Cleaned siesta and VASP reading of completed jobs, 287

- added Geometry.new allowing easy type-lookups to convert to Geometry
e.g. Geometry.new("RUN.fdf") and Geometry.new(ase_atoms) automatically
figures out which method to call and how to interpret the objects.
added Geometry.to allowing easy type-lookups to convert to other objects
282

- enabled calculating supercell matrices with phases, format=sc:<format>
returns in supercell matrix form (no, no_s)

- removed support for int and long as matrix types, only float/complex

- Enabled `sgrid` to write tables of data

- Merged spin_orbital_moment(deleted) and spin_moment with
optional argument project

- Enabled orbital resolved velocities

- Added outSileSiesta.read_energy to read final energies in a property-dict
(works both as a property (`energy.fermi`) and a dictionary (`energy["fermi"]`)

- Ensured ghost atoms in Siesta are handled with separate
class, AtomGhost, 249

- Using `si.RealspaceSI` with `unfold=(1,1,1)` no longer results in `nsc` on
the given surface hamiltonian being set to `(1,1,1)`.

- Added calculation of isosurfaces, 246

- Added `sisl.WideBandSE` for self-energies with constant
diagonals

- Enabled more user control over categories, 242

- Improved interpolation function for Grid's, and also
added filters

- Bugfix for periodic directions for ASE conversion, 231

- Fixed tuples for `_sanitize_atoms`, 233

- Fixed reading correct unit from deltanc files, 234

- Enabled berry-phase calculations for NC+SOC, 235

- Added tiling to Grid, 238

- Added Atoms.group_data which nicely splits an array holding
orbital information into atomic contributions (a list since
each sub-list may be unequal in length)

- Many small bug-fixes and performance improvements

- Exposing sisl_toolbox as a module for external contributions
Now stuff contributed from 3rd parties can easily be included
in a toolbox which is a separate module.

- Changed asarray (as*) methods for SparseGeometry
Now we have a dispatch class which enables one
to store the behaviour as variables and then post-process

- Using `*.geom` or `geometry.atom` is now deprecated, use
`*.geometry` and `geometry.atoms` instead (respectively)

- Added spin-rotation for density matrices, this will
enable sisl to manipulate DM and write them for
Siesta calculations

- Enabled all numpy.ufuncs (np.exp(H))

- Added nanoribbons construction (tfrederiksen)

- Internal change to pathlib for files and paths

- Added velocity calculations for NC+SOC Hamiltonians

- Sparse pattern transposes of non-full matrices, fixed bug

- Changed Geometry.sort to be more diverse (this may break old code)
This new way of sorting is way more flexible and allows very fine
control, fixes 191, 197

- Added a bilayer geometry which can create twisted bilayers 181, 186

- Enabled VASP `*CAR` files to write/read dynamic specifications 185

- Enabled `xarray.DataArray` returning from BrillouinZone objects 182

- Several improvements to outSileSiesta.read_scf 174, 180

- A huge performance increase for data extraction in tbtncSileTbtrans
(thanks to Gaetano Calogero for finding the bottleneck)

- Added preliminary usage of Mixers, primarily intented for extending
sisl operations where SCF are used (may heavily change).

- Lots of small bug-fixes

- Now sisl is Python >=3.6 only, 162

This release was helped by the following committers (THANKS):

- Thomas Frederiksen
- Pol Febrer
- Jonas Lundholm Bertelsen
- Bernhard Kretz

- fixed 160 by removing all(?) TRS k-points in a Monkhorst Pack grid

- fixed repeat for SparseGeometryOrbital 161

- changed lots of places for einsum in electron.py for increased performance

- added AHC conductivity calculations `conductivity` (not tested)

- added Berry curvature calculations `berry_flux` (not tested)

- added Overlap class to directly use overlap matrices (without having a
second matrix).

- fixed geometry align issue when reading geometries from Siesta output 153

- fixed pickling a sparse matrix 150

- Fixed TSV.nc write-out for grid files (see poisson_explicit.py)

- Fixed fermi level calculation for non-polarized calculations

- Reverted Fermi calculation routine for more stable implementation

- fixed DynamiclMatrix reading for number of atoms not divisable by 4 145

A huge thanks to Jonas L. B. for fixes, suggestions etc.