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.

v0.8.4

• 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.

v0.8.3

• 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.

v0.8.2

You are encouraged to update to this release which introduces many performance improvements and bug-fixes.

• 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.

v0.8.1

You are heavily encouraged to update as this incorporates many new features and bug-fixes.

• 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.

• Shapes 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

v0.8.0

I am proud to announce the release of sisl 0.8.0.

Since this version one may easily install sisl using pypi or conda:

pypi install sisl
conda install -c zerothi sisl

Release notes

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(dR, param)
  Hamiltonian.construct(func)
  or
  Hamiltonian.construct((dR, 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!

v0.7.6

API updates for Siles.

This release enhances the use of the implicit siles in sisl with a more stringent file name.

• Added sdata script which parses the arguments based on the input file. This is preliminary work and will still change
• Added XSF file format
• Added bands file from siesta to easily plot band structures using python
• Many bug-fixes for the IO of geometry read/write in rarely used file formats
• Speeded up the Hamiltonian creation
• Added code-coverage tests (mainly for developing reasons)

v0.7.5

Added Wannier90 support (reading of Wannier-Hamiltonian and Wannier-centres)

Enabled multiple Sile extensions with the same extension (by requesting specific classes).

Fixed things related to overlap matrices in the Hamiltonian structure. Added a few tests about the Hamiltonian.