0.14.0

Released 28 of September 2023.

Contributors

A total of 4 people contributed to this release. People with a “+” by their names contributed a patch for the first time.

  • Nick Papior

  • Nils Wittemeier

  • Pol Febrer

  • Thomas Frederiksen

Pull requests merged

A total of 30 pull requests were merged for this release.

  • #421: Function to build heteroribbons

  • #476: Refactoring the viz module to a more modular design.

  • #528: bug: outSile.read_scf was not able to read unconverged SCF loops

  • #531: enh: Added Nodes and Workflows.

  • #533: bug: functions could not overwrite node arguments

  • #534: Add env variable to docs build

  • #540: bug: fixed swapaxes handling

  • #542: mnt: changed only= keyword arguments to what=

  • #544: aniSileSiesta

  • #546: mnt: added geometry collection with some more features

  • #547: mnt: nodes context settings are no longer a regular input

  • #549: Bugfix for rotate(…, atoms=list) + additional tests

  • #550: changed SuperCell to Lattice, long overdue

  • #562: Wrap fortran files import in try/except block.

  • #563: Scikit build core

  • #566: Make documentation tabs more visual

  • #573: VASP forces from OUTCAR

  • #575: cleaned the procedure for locating maxR

  • #581: undo change of filenames

  • #585: translate2uc for sparse matrices with associated geometries.

  • #586: Slicing IO read_* routines

  • #589: removed Collection + GeometryCollection

  • #594: Fix missing import in siesta_grid.

  • #596: netCDF4 is now an optional dependency

  • #598: maint: Adapt to breaking changes in scipy.sparse.isspmatrix

[0.14.0] - 2023-09-28

Added

  • added SISL_UNIT_SIESTA to select between legacy or codata2018 units (since Siesta 5) New default is codata2018, may create inconsistencies until Siesta 5 is widely adopted.

  • added –remove to sgeom for removing single atoms

  • added a EllipticalCylinder as a new shape

  • added basis-enthalpy to the stdoutSiestaSile.read_energy routine

  • added read_trajectory to read cell vectors, atomic positions, and forces from VASP OUTCAR

  • slicing io files multiple output (still WIP), see #584 for details Intention is to have all methods use this method for returning multiple values, it should streamline the API.

  • allowed xyz files to read Origin entries in the comment field

  • allowed sile specifiers to be more explicit:

    • “hello.xyz{contains=<name>}” equivalent to “hello.xyz{<name>}”

    • “hello.xyz{startswith=<name>}” class name should start with <name>

    • “hello.xyz{endswith=<name>}” class name should end with <name> This is useful for defining a currently working code:

      SISL_IO_DEFAULT=siesta

  • added environment variable SISL_IO_DEFAULT which appends a sile specifier if not explicitly added. I.e. get_sile("hello.xyz") is equivalent to get_sile("hello.xyz{os.environ["SISL_IO_DEFAULT"]}". Fixes #576

  • added a context manager for manipulating the global env-vars in temporary locations. with sisl_environ(SISL_IO_DEFAULT=...)

  • enabled Geometry.append|prepend in sgeom command (reads other files)

  • added fdfSileSiesta.write_brillouinzone to easily write BandLines to the fdf output, see #141

  • added aniSileSiesta for MD output of Siesta, #544

  • mdSileOpenMX for MD output of OpenMX

  • Atoms.formula to get a chemical formula, currently only Hill notation

  • unified the index argument for reading Grids, read_grid, this influences Siesta and VASP grid reads.

  • sisl.mixing:

    • AndersonMixer enables the popular and very simple linear-like mixer

    • StepMixer allows switching between different mixers, for instance this

      enabled restart capabilities among other things.

    • Enabled composite mixers (simple math with mixers)

  • BrillouinZone.merge allows simple merging of several objects, #537

Changed

  • updated the viz module, #476

  • allowing ^ negation in order arguments for siles

  • internal change to comply with scipy changes, use issparse instead of spmatrix, see #598

  • netCDF4 is now an optional dependency, #595

  • interface for Sparse*.nonzero(), arguments suffixed with ‘s’

  • stdoutSileVASP will not accept all= arguments

  • stdoutSileVASP.read_energy returns as default the next item (no longer the last)

  • txtSileOrca will not accept all= arguments, see #584

  • stdoutSileOrca will not accept all= arguments, see #584

  • xyzSile out from sisl will now default to the extended xyz file-format Explicitly adding the nsc= value makes it compatible with other exyz file formats and parseable by sisl, this is an internal change

  • default of Geometry.translate2uc, now only periodic axes are default to be moved

  • all out files have been renamed to stdout to clarify they are user determined output file names, suggestion by @tfrederiksen

  • bumped Python requirement to >=3.8

  • orbitals R arguments will now by default determine the minimal radii that contains 99.99% of the function integrand. The argument now accepts values -1:0 which is a fraction of the integrand that the function should contain, a positive value will explicitly set the range #574

  • Added printout of the removed couplings in the RecursiveSI

  • SuperCell class is officially deprecated in favor of Lattice, see #95 for details The old class will still be accessible and usable for some time (at least a year)

  • Enabled EigenState.wavefunction(grid) to accept grid as the initialization of the grid argument, so one does not need to produce the Grid on before-hand

  • Geometry.rotate(only=) to (what=), this is to unify the interfaces across, #541 Also changed the default value to be “xyz” if atoms is Not none

  • tbtncSileTBtrans(only=) arguments are changed to (what=) #541

  • SelfEnergy.scattering_matrix is changed to SelfEnergy.broadening_matrix ince the scattering matrix is an S-matrix usage. Also changed se2scat to se2broadening #529

  • allow BrillouinZone initialization with scalar weights for all k-points #537

  • Geometry.swapaxes and SuperCell.swapaxes, these are now more versatile by allowing multiple swaps in a single run, #539

  • deprecated set_sc

  • internal build-system is changed to scikit-build-core, the distutils will be deprecated in Python>=3.12 so it was a needed change. This resulted in a directory restructuring.

Fixed

  • fixed Mulliken calculations for polarized calculations due to missing copy, #611

  • fixed single argument ret_isc=True of close, #604 and #605

  • tiling Grid now only possible for commensurate grids (grid.lattice % grid.geometry.lattice)

  • rare cases for non-Gamma calculations with actual Gamma matrices resulted in crashes #572

  • MonkhorstPack.replace now checks for symmetry k-points if the BZ is using trs. Additionally the displacements are moved to the primitive point before comparing, this partly fixed #568

  • spin-orbit Hamiltonians in RealSpaceSE and RealSpaceSI, fixes #567

  • ufunc reductions on SparseGeometry where axis arguments reduces dimensionality

  • interaction with pymatgen

  • fdfSileSiesta.includes would fail when empty lines were present, #555 fixed and added test

  • Documentation now uses global references

  • Geometry.swapaxes would not swap latticevector cartesian coordinates, #539

toolbox.btd

Added

  • calculation of scattering matrices