Sisl

- 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

- Fixed scaling of bond-currents in case 'all' is used, makes comparison
with '+' and '-' easier.

- Updated defaults in bond_current to '+' such that only forward
going electrons are captured.

- Updated defaults in vector_current to '+' such that only forward
going electrons are captured.

- Enabled reading a tabular data-file

- Lots of updates to the spin-class. It should now be more coherent.

- Added rij and Rij to the sparse_geometry classes to extract orbital or
atomic distance matrices (returing the same sparsity pattern).

- Renamed `which` keyword in `Geometry.center` to `what`

- Added uniq keyword to o2a for better handling of orbitals -> atoms.

- Fixed a performance bottleneck issue related to the `scipy.linalg.solve`
routine which was changed since 0.19.0.

- Changed internal testing scheme to `pytest`

- Lots of bug-fixes here and there

- Geometry files used in the command-line has updated these arguments:

- tile
- repeat
- rotate

The order of the arguments are interchanged to be similar to the
scripting capabilities.

Also fixed an issue related to moving atoms into the unit-cell.

- Enabled deleting supercell elements of a sparse Geometry. This
will come in handy when calculating the self-energies and Green
functions. I.e. Hamiltonian.set_nsc(...) will truncate entries
based on the new supercell.

- Preliminary testing of reading Siesta binary output (.RHO, .VT, etc.)

- Added parsing the Siesta EIG file (easy plotting, reading in Python)

- Changed interface for BrillouinZone objects.
Now a BrillouinZone accepts any object which has cell/rcell entries.
Any function call on the BrillouinZone object will transfer the call to the
passed object and evaluate that function for all k-points in the BrillouinZone.

- sisl.io.siesta.tbtrans

* Added current calculator to TBT.nc sile to calculate the current as TBtrans
does it (this requires the latest commit in SIESTA which defines the
chemical potential and electronic structure of *all* electrodes).

* Bug-fixes for TBT.nc sile, the bond-currents for multi-orbital systems
were in some cases wrong.

* Huge performance increase for TBT.nc data processing. Now the majority
of routines are based on array-indexing, rather than sparse loops.

* Changed the DOS retrieval functions to be more flexible. The default is
now to return the summed DOS across the selected atoms.

* Added a TBTGFSileSiesta which enables one to create _external_ self-energies
to be read in by TBtrans (complete electrode control).

* Added `deltancSileSiesta` as a replacement for `dHncSileSiesta`, TBtrans 4.1b4
will have two delta terms, dH (adds to bond-currents) and dSigma (does not
add to bond-currents).

* BEWARE, lots of defaults has changed in this release.

- Hamiltonian.tile is now even faster, only utilizing
intrinsic numpy array functionality.

- Greatly speeded up Hamiltonian.remove/sub functions.
Now there are no for-loops in the remove/sub routines which
will greatly increase performance.
It will now be much faster to generate the Hamiltonian for
a small reference cell, tile/repeat it, remove atoms.

- Added the following routines:

* `SuperCell.fit` routine to determine a new supercell object
such that a given set of coordinates are all within AND
periodic in the new supercell.
* `SuperCell.parallel` to check whether two objects have parallel
latticevectors.
* `Geometry.distance` returns a list of distances from a given
set of atoms. I.e. to determine a set of distances required for
a subsequent close call. This routine can also be used to group
neighbouring atoms in a common fashion.
* `Geometry.optimize_nsc` loops all atoms and minimizes `nsc` in case
one is not sure of the interaction range.
* `Hamiltonian.shift` enables the shift of the entire electronic structure
Fermi-level.
* Added new flag to `Hamiltonian.Hk` routines
``format={'csr', 'array', 'dense', ...}``
to ensure a consistent return of the data-type.

- Bug fix for dHncSileSiesta for multiple levels.

- Performance boost for the sub and remove functions for the
Hamiltonian objects. Instead of creating the geometry first,
it may now be much faster to generate the small Hamiltonian,
tile -> repeat -> sub -> remove.

- Performance boost for the tile and repeat functions for the
Hamiltonian objects. They are now the preferred method for creating
large systems.

- Bug fixed when having extremely long atomic ranges and using tile/repeat.
The number of supercells was too large.
It did not affect anything, but it was inconsistent.

- Enabled reading the density matrix and energy density matrix from siesta.

- Addition of a PerformanceSelector class which enables a dynamic
selection of the best routine.

Currently this is enabled in the SparseOrbitalBZ class where
constructing a matrix k can be done in numerous ways.

- Bug fixed in supercell specification of the Hamiltonian:

>>> H[io, jo, (-1, 0, 0)]

now works in all cases.

- Spin-orbit H(k) has been enabled

- Fixed reading the <>.nc file from SIESTA, the non-zero elements count was
wrong.

- Now H(k) has been tested for non-colinear and spin-orbit coupling and
one can now use sisl to perform non-colinear and spin-orbit coupling
calculations.

- API change, all dR keywords has been changed to R for consistency and
reduction of ambiguity.
Also the `Atoms.dR` is now referred to as `Atoms.maxR()` to indicate
its meaning.

This may break old scripts if one use the `dR` keyword in arguments.