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v0.9.4
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@zerothi zerothi released this 04 Aug 19:41
v0.9.4
2c8522a

  • 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

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