CHANGELOG

0.9.7
=====

- 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.


0.9.6
=====

- 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

0.9.5
=====

- 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

0.9.4
=====

- 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


0.9.2
=====

- Various minor bug-fixes

0.9.1
=====

- 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.

0.9.0
=====

- 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.


0.8.5
=====

- 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.


0.8.4
=====

- Added BrillouinZone class to easily create BrillouinZone plots etc.
  When calculating the eigenspectrum of a Hamiltonian one may pass
  the BrillouinZone object instead of the k-point to retrieve all
  eigenvalues for the k-points in the BrillouinZone object.
  Say for a PathBZ one can now easily retrieve the band-structure.

- Enabled specification of Hamiltonian connections across supercells via
  a tuple index (as the last index):

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

  Thus connecting orbital `io` and `jo` across the -1 first lattice vector

- Enabled tbtrans files to attach a geometry (to get correct species).

- API change of:

      read/write_geom => read/write_geometry
      read/write_sc => read/write_supercell
      read/write_es => read/write_hamiltonian

  Moved `quantity` to `physics`.

- Enabled slice deletion in `SparseCSR`

  Enabled eliminate_zeros() to remove unneeded values.

- Added ScaleUp compatibility. sisl now acceps ScaleUp files which is
  a 2nd principles code for large scale calculations using Wannier
  functions.

- Added Hamiltonian.sub/remove/tile for easy extension of Hamiltonian
  without having to construct the larger geometries.
  This should speed up the creation of really large structures
  as one may then simply "update" the Hamiltonian elements subsequently.


0.8.3
=====

- Fixed bug in __write_default (should have been _write_default)

- API change in `close` functions, now ret_coord => ret_xyz,
  ret_dist => ret_rij

- Added `SparseCSR` math operations work on other `SparseCSR` matrices
  Thus one may now do:

      >>> a, b = SparseCSR(...), SparseCSR(...)
      >>> aMb, aPb = a * b, a + b

  Which makes many things much easier.
  If this is used, you are encouraged to assert that the math is correct.
  Currently are the routines largely untested. _Assistance is greatly appreciated
  in creating `nosetests`_.

- Geometries now _always_ create a supercell. This was not the case when
  an atom with no defined orbital radius was used. Now this returns a
  supercell with 10 A of vacuum along each Cartesian direction.


0.8.2
=====

- Fixed reading _hr.dat from Wannier90, now the band-structure of
  SrTiO3 (Junquera's test example) is correct.

- Speeded up tbtrans.py analyzing methods enourmously by introducing
  faster sparse iterators. Now one can easily perform data-analysis on
  systems in excess of 10.000 atoms very fast.

- Added the TBT.AV.nc file which is meant to be created by `sisl` from
  the TBT.nc files (i.e. create the k-averaged output).
  This enables users to run tbtrans, create the k-averaged output, and
  then delete the old file to heavily reduce disk-usage.

  An example:

      tbtrans RUN.fdf > TBT.out
      sdata siesta.TBT.nc --tbt-av
      rm siesta.TBT.nc

  after this `siesta.TBT.AV.nc` exists will all k-averaged quantites.
  If one is not interested in k-resolved quantities this may be very interesting.

- Updated the TBT.nc sile for improved readability.

- Easier script data-extraction from TBT.nc files due to easier conversion
  between atomic indices and pivoting orbitals.

  For this:
  * a2p
    returns the pivoting indices for the given atoms (complete set)
  * o2p
    returns the pivoting indices for the given orbitals

  * Added `atom` keyword for retrieving DOS for a given set of atoms

  * `sdata` and `TBT.nc` files now enable the creation of the TBT.AV.nc file
    which is the k-averaged file of TBT.nc

- Faster bond-current algorithms (faster iterator)

- Initial template for TBT.Proj files for sdata processing

- Geometry:

  * Enabled multiplying geometries with integers to emulate `repeat` or
    `tile` functions:

        >>> geometry * 2 == geometry.tile(2, 0).tile(2, 1).tile(2, 2)
        >>> geometry * [2, 1, 2] == geometry.tile(2, 0).tile(2, 2)
        >>> geometry * [2, 2] == geometry.tile(2, 2)
        >>> geometry * ([2, 1, 2], 'repeat') == geometry.repeat(2, 0).repeat(2, 2)
        >>> geometry * ([2, 1, 2], 'r') == geometry.repeat(2, 0).repeat(2, 2)
        >>> geometry * ([2, 0], 'r') == geometry.repeat(2, 0)
        >>> geometry * ([2, 2], 'r') == geometry.repeat(2, 2)

    This may be considered an advanced feature but useful nonetheless.

  * Enabled "adding" geometries in a similar way as multiplication
    I.e. the following applies:

        >>> A + B == A.add(B)
        >>> A + (B, 1) == A.append(B, 1)
        >>> A + (B, 2) == A.append(B, 2)
        >>> (A, 1) + B == A.prepend(B, 1)

  * Added `origo` and `atom` argument to rotation functions. Previously this could be
    accomblished by:

        rotated = geometry.move(-origo).rotate(...).move(origo)

    while now it is:

        rotated = geometry.rotate(..., origo=origo)

    The origo argument may also be a single integer in which case the rotation
    is around atom `origo`.

    Lastly the `atom` argument enables only rotating a sub-set of atoms.

  * Geometry[..] is now calling axyz if `..` is pure indices, if it is
    a `slice` it does not work with super-cell indices

  * Added `rij` functions to the Geometry for retrieving distances
    between two atoms (`orij` for orbitals)

  * Renamed iter_linear to iter

  * Added argument to iter_species for only looping certain atomic indices

  * Added iter_orbitals which returns an iterator with atomic _and_ associated
    orbitals.
    The orbitals are with respect to the local orbital indices on the given atom

    ```
    >>> for ia, io in Geometry.iter_orbitals():
    >>>     Geometry.atom[ia].R[io]
    ```

    works, while

    ```
    >>> for ia, io in Geometry.iter_orbitals(local=False):
    >>>     Geometry.atom[ia].R[io]
    ```

    does not work because `io` is globally defined.

  * Changed argument name for `coords`, `atom` instead of the
    old `idx`.

  * Renamed function `axyzsc` to `axyz`

- SparseCSR:

  * Added `iter_nnz(i=None)` which loops on sparse elements connecting to
    row `i` (or default to loop on all rows and columns).

  * `ispmatrix` to iterate through a `scipy.sparse.*_matrix` (and the `SparseCSR`
    matrix).

- Hamiltonian:

  * Added `iter_nnz` which is the `Hamiltonian` equivalent of `SparseCSR.iter_nnz`.
    It enables explicit looping on atomic couplings, or orbital couplings.
    I.e. one may specify a subset of atoms or orbitals to loop over.

  * Preliminary implementation of the non-collinear spin-case. Needs testing.

0.8.1
=====

- Fix a bug when reading non-Gamma TSHS files, now the
  supercell information is correct.

- tbtncSileSiesta now distinguishes between:
    electronic_temperature [K]
  and
    kT [eV]
  where the units are not the same.

- Fixed TBT_DN.nc TBT_UP.nc detection as a `Sile`

- Added information printout for the TBT.nc files

       sdata siesta.TBT.nc --info

  will print out what information is contained in the file.

- `Atoms` overhauled with a lot of the utility routines
  inherent to the `Geometry` object.
  It is now much faster to perform operations on this
  object.

- The FDF sile now allows setting and retrieving variables
  from the fdf file. Hence one may now set specific
  fdf flags via:

       sdata RUN.fdf --set SolutionMethod Transiesta

- Changed default output precision for TXT files to .8f.
  Additionally one may use flag `--format` in `sgeom` to
  define the precision.

- `Shape`s have been added. There are now several Shapes
  which may be used to easily find atoms within a given Shape.
  This should in principle allow construction of very complex Shapes
  and easier construction of complex Hamiltonians


0.8.0
=====

This release introduces many API changes and a much more stream-lined
interface for interacting with sisl.

You are heavily encouraged to update your distribution.

Here is a compressed list of changes:

- sdata is now an input AND output dependent command.
  It first reads the input and output files, in a first run, then
  it determines the options for the given set of files.
  Secondly, the sdata command uses "position dependent" options.
  This means that changing the order of options may change the output.
- tbtncSile
  * Correct vector currents (for xsf files)
  * bug-fix for Gamma-only calculations
  * returned DOS is now correctly in 1/eV (older versions returned 1/Ry)
  * fixed sdata atomic[orbital] ranges such that, e.g. `--atom [1-2][3-5]`
    (for atom 1 and 2 and only orbitals 3, 4 and 5 on those atoms.)
  * DOS queries now has an extra argument (E) which returns only for the
    given energy.
  * When storing tables in sdata this now adds information regarding
    each column at the top (instead of at the bottom).
    Furthermore, the information is more descriptive
- Changed all `square` named arguments to `orthogonal`
- Added nsc field to xyz files (to retain number of supercells)
- Added `move` function for geometry (same as translate)
- Added `prepend` function, equivalent to `append`, but adding the
  atoms in the beginning instead of the end
- Fixed many bugs related to the use of Python-ranges (as opposed to numpy ranges)
- SparseCSR now enables operations:
    a = SparseCSR(...)
    a = a * 2 + 2
  is now viable. This enables easy scaling, translation etc. using the
  sparse matrix format (very handy for magnetic fields).
- Enabled `del` for SparseCSR, i.e. `del SparseCSR(..)[0, 1]` will
  remove the element, completely.
- Enabled reading of the TSHS file from SIESTA 4.1, now we may easily interact
  with SIESTA.
- Moved version.py to info.py
- Moved scripts to `entry_points`, this makes scripts intrinsic in the module
  and one may import and use the commands as their command-line equivalents.
- Hamiltonian.construct now takes a single argument which is the function
  for the inner loop.
  The old behaviour may be achieved by doing either:
  >>> func = Hamiltonian.create_construct(R, param)
  >>> Hamiltonian.construct(func)
  or
  >>> Hamiltonian.construct((R, param))
- The atoms contained in the Geometry are now not duplicated in case of many
  similar Atom objects. This should reduce overhead and increase throughput.
  However, the efficiency is not optimal yet.
- Added many more tests, thus further stabilizing sisl

  I would really like help with creating more tests!
  Please help if you can!


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