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@zerothi zerothi released this 31 Mar 20:07
· 4329 commits to main since this release
v0.8.2
374140b

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.

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