v0.11.0

• 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:
  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

Contributors

A total of 5 people contributed to this release.

• Jonas Lundholm Bertelsen
• Nick Papior
• Pol Febrer
• Sofia Sanz Wuhl
• Thomas Frederiksen

Pull requests merged

A total of 12 pull requests were merged for this release.

• #231 <https://github.com/zerothi/sisl/pull/231>__: Transmitting pbc to ASE
• #246 <https://github.com/zerothi/sisl/pull/246>__: Method to calculate grid isosurfaces
• #253 <https://github.com/zerothi/sisl/pull/253>__: Geometry._sanitize_atoms did not accept generic categories
• #254 <https://github.com/zerothi/sisl/pull/254>__: f-string was not printing variable value due to missing f
• #255 <https://github.com/zerothi/sisl/pull/255>__: Make parent categories callable and avoid their instantiation
• #258 <https://github.com/zerothi/sisl/pull/258>__: Making coordinate categories more accessible
• #263 <https://github.com/zerothi/sisl/pull/263>__: Supporting the creation of Binder docker images
• #267 <https://github.com/zerothi/sisl/pull/267>__: bug: skewed isosurfaces were not properly calculated
• #270 <https://github.com/zerothi/sisl/pull/270>__: Fixed reading geometries in .AXSF-files
• #277 <https://github.com/zerothi/sisl/pull/277>__: maint: remove ending blank line when writing xyz-files
• #298 <https://github.com/zerothi/sisl/pull/298>__: All plotly tests passing now
• #300 <https://github.com/zerothi/sisl/pull/300>__: Make plotly docs work

v0.10.0

• 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 (Thomas)

• 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

v0.9.8

THIS WILL BE THE LAST Python2 release.
All subsequent releases will be Python 3.6 and later (only!).

• 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.

v0.9.7

• 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.

v0.9.6

• 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

v0.9.5

• 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

v0.9.4

• 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

v0.9.1

• 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.

v0.9.0

• 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.

v0.8.5

• 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.