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.

v0.7.1

Enabled orthogonal Hamiltonian objects.

Implemented dH.nc file for TBtrans code.

v0.7.0

Initial release of sisl with proper DOI citation using Zenodo.

Changes:

• Restructuring of the contained Sile's of the different linked DFT programs.