Sisl

- Bug-fix for reading geometries in outSiesta

- Enabled reading the fermi level from the output, fixes 126

- Enabled Siesta STM and STS output

- Fixed an inheritance issue in `axsfSile` which meant it was unusable until
now

- Maintenance fix for looping sparse matrices.
Now the default is to loop the sparse non-zero elements.
If one wishes to loop all atoms/orbitals one should use `iter_orbitals()`
NOTE: This *may* break some codes if they used loops on sparse matrices

- Fixed reading VASP CAR files with constraints (thanks to T. Frederiksen)

- Added `overlap` method to `Geometry` to find overlapping atoms
between two geometries.

- Added Siesta LDOS charge handling

- Changed edges method to not exclude it-self by default.
This is because it is not intuitive given the default exclude=None

Note: this may break compatibility with other software/scripts.

- Added mulliken charge calculations and orbital angular momentum
for SO DM, fixes 136

- Fixed reading overlap matrix in conjunction with DM from fdf-sile

- Performance increase for the real-space self-energy calculations

- Fixed transposing of the spin-box for NC and SO matrices

- Enabled TRS handler for SO matrices, fixes 125

- Enabled better b-casting assignments for sparse-matrices, fixes 134

- Upgraded documentation to a layout that obeys numpydoc

- Fixed reading ASE xyz outputs, thanksto JL. Bertelsen,

- Fixed a typo in fdf reading onlyS, thanks to JL. Bertelsen, 135

- Enabled reading arbitrary self-energy by requesting an energy and k-point
from TSGF files.

- Upgraded handling of TBT.*.nc files to conform with the >=Siesta-4.1-b5
releases where all files contain the same device + electrode meta-data.

- Deprecated TBTGFSileTBtrans (use tbtgfSileTBtrans instead)

- Forced align=False in inner such that users should take care of this

- Added align_norm to swap states such that they more or less
correspond to the same band (which should have a closer residual
for on-site coefficients).

- Removed norm2 and made norm equal to norm2 for states. This is
the more natural thing, besides. Doing norm() ** 0.5 shouldn't be
too much of a problem.

- Officially added real-space self-energy calculations

- Cleaned TBT vs. PHT for class name structures

- Bugfix for reading MD output from Siesta out-files 130

- Bugfix for tbtse files when requesting pivoting indices using this
combination ``in_device=True, sort=False`` which in most cases
return wrong indices, thanks to J. Bertelsen for bug-find!

- Added several routines for retrieving transposed coupling elements.
When having connections `i -> j` it may be beneficial to easily get
the transposed connection `j -> i` by taking into account the
supercell. `Geometry.a2transpose` enables this functionality making
construct functions much simpler when having edges/boundaries.

- Bug-fix for reading white-space prefixed keywords in XSF files, 127

- Performance increase for self-energy calculations for very small
systems

- Huge memory reduction for `Geometry.o2a` with very large system

- Enabled pickling on `BrillouinZone` objects

- Added `spin_moment` to `Hamiltonian`

- Removed ``rotate[abc]`` methods since they were cluttering the name-space
Codes should simply replace with:

>>> geometry.rotate(angle, geometry.cell[{012}, :], *)

for the same effect.

- Finally removed deprecated `write_geom` from the API

- Enabled calculation of ``<S^2>`` for spin-polarized calculations, this
may be used for calculating spin-contaminations

- added checks for `SparseCSR` to disallow out-of-bounds keys

- Bug fixed for reading POSCAR files from VASP (only when multiple species are
used in a non-ordered fashion)

- added `sisl` command line utility, it is exactly the same as `sdata`

- Enabled pickling sparse matrices, this allows dask usage of sparse matrices

- Performance increase for sparse matrix handling

- Fixed a problem with Fortran IO + Jupyter notebooks, now the file-handles
are re-used if a code block is terminated before closing the file

- Added `SparseOrbital` `append` + `transpose`
This enables appending Hamiltonian's (append) and makes hermiticity
checks possible (transpose)

- Enabled complex averaged calculations using `oplist`
The `oplist` object is a container allowing inter-element operations

>>> l1 = oplist([0, 1])
>>> l2 = oplist([2, 3])
>>> l = l1 + l2
>>> print(l)
[2, 4]

This is extremely handy for `BrillouinZone.asaverage`/`assum` when calculating
multiple values using `eigenstate` objects.

- Added reflection calculation to `tbtncSileTBtrans`

- Added more distribution functions (step and heaviside)

- Removed numpy deprecated class numpy.matrix, now everything is array

- Removed possibility of using `kavg=list(...)` due to complexity, now single
`kavg` requests are *not* k-averaged.

- Bugfix in calculating `shot_noise`, `noise_power` and `fano` factors in `tbtncSileSiesta`
They were only correct for Gamma-point calculations

- Fixed `*.EIG` `sdata` processing when using `--dos`

- Fixed reading geometries from grids from VASP (grid values were correct)

- Toolboxes:

* Added a toolbox to calculate the Poisson solution for arbitrary
electrodes for TranSiesta

- Fixed temperature for phonon output pht*nc files

- Added tbtprojncSileTBtrans sile for analyzing projected transmissions

- Removed deprecated dhSileTBtrans

- Bug fix for binary grid files with Siesta and also reads using fdf-files

- Changed default self-energy eta values to 1e-4 eV

- Added Zak-phase calculations (thanks to T. Frederiksen)

- Updated lots of State methods

- added Bloch expansion class which can expand any method

- self-energy calculations:
- Much faster
- enabled left/right self-energies in one method

- fixed AtomicOrbital copies

- enabled TSGF reads

- Added noise-power calculations for TBT.nc files

- Fixed TBT.SE.nc files, units and scattering matrix retrieval

- added more VASP files

- Fixes for the GULP dynamical matrix reads

- Enabled preliminary reads of OpenMX input file

- Enabled DOS calculation for the eigenvalue files

- Added Berry-phase calculation for orthogonal basis sets

- Added velocity calculation of electronic eigenstates

- Enabled effective mass tensor in electronic eigenstates (un-tested)

- High performance increase by moving stuff to Cython.

- Added Siesta interaction tutorials

- Added orthogonality checks when reading sparse matrices

- Lots of fixes for the fdf-file

- Added Mulliken calculation in DensityMatrix/EnergyDensityMatrix

- Enabled reading phonons from FC files

- Added named-groups which enables accessing groups of atoms by names.

Geometry['Hello'] = [2, 3, 4]

- Changed Hessian to DynamicalMatrix to clarify the units

- Added new units class to handle complex units.

- Enabled a Phonon class to calculate group velocities of phonons, DOS and PDOS,
displacements

- Bug-fixes for Siesta binary writes, now the supercell format is *always*
Siesta compliant.

- Enabled replacing k-points in MonkhorstPack grids.

- Enabled calculation of band-velocities from eigenstates

- Made better progress-bars. Using eta= now relies on tqdm
It is however still an optional dependency.

- Fixed Gamma-point periodic wavefunction storage.
Creating grids with wave-functions is fully functional
for arbitrarily big supercells.

- BrillouinZone objects:

- Renamed PathBZ to BandStructure

- Renamed MonkhorstPackBZ to MonkhorstPack

- Enabled MonkhorstPack symmetry. This will reduce the number of
k-points to roughly half (note symmetry is by default *on*)

- Forced MonkhorstPack to create a k-grid which is Gamma centered

- Shapes (backwards compatibility broken)

- Complete re-write of Shapes

- Skewed Cuboids, Ellipsoids

- Set combinations of Shapes (unions, difference sets, etc.)

- Grid

- Enabled Grid.index for shapes.

- Fixed grid initialization to create grid spacings fixed by a real.
I.e. the voxel spacing.


>>> Grid([10, 10, 10]) 10 points per lattice vector
>>> Grid(0.1) 0.1 Angstrom spacing

- Enabled plotting wavefunctions on grids.

- Enabled plotting charge density on grids.

- Enabled tqdm usage for progressbar. It is fast and easy to use
and a small requirement. (still optional)

- Added intrinsic Sisl exceptions which will be used throughout
(at some point)

- Removed deprecated TightBinding class (use Hamiltonian instead)

- Added many SislWarning raises which are used to notify the user of
potentially important things (say if sisl knows there should be a unit
associated but it couldn't find it).

- Added TSDE file reading in sisl.

- Siesta reading of grid-related data is now much *smarter*. It will
try and recognize the units of the data so the units become sisl
intrinsics (Ry -> eV, Bohr -> Ang, etc.).
This means that typically one does not need to do manual unit-conversion.
There are however a few cases where sisl cannot figure out the
units. Particularly if the files are renamed.

- Added a new class EigenSystem which holds information regarding
eigenvalues and eigenvectors.

- Currently an EigenState class is also enabled which can currently
be used to calculate wavefunctions, DOS, PDOS and more to come.

- Fixed lots of bugs in fdf-reading quantities.
Now one is also able to read Hamiltonian and other physical
quantities from the fdf-object directly. There is pre-defined
orders of which files to read from if there are multiple files
eligeble.

Reading the geometry now defaults to the fdf file, but one can query
the output files by a boolean.

- Enabled PDOS calculations for the Hamiltonian. Together
with the MonkhorstPack class one can easily calculate
k-averaged PDOS quantities.

- Fixed cube reading/writing of multi-column data.

- Added siesta PDOS xml parsing, currently this is only scriptable
but it manages easy extraction of quantities without the PDOSXML utility.
This also enables retrieving the PDOS as an xarray.DataArray.

- Fixed a bug in writing XV files (only for -100/-200 species)

- TBtrans / TBT.nc file:

- Added TBT.SE.nc file to enable easy extraction of self-energies
from TBtrans

- Added COOP and COHP extraction to the TBT.nc files.

- Added DM and ADM extraction to the TBT.nc files.

- Reorganized the TBtrans netcdf files (internal changes only)

- Added shot-noise calculation (and Fano factor). Currently un-tested!

- Several added files

- Various minor bug-fixes