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| 1 | +****** |
| 2 | +0.14.0 |
| 3 | +****** |
| 4 | + |
| 5 | +Released 28 of September 2023. |
| 6 | + |
| 7 | + |
| 8 | +Contributors |
| 9 | +============ |
| 10 | + |
| 11 | +A total of 4 people contributed to this release. People with a "+" by their |
| 12 | +names contributed a patch for the first time. |
| 13 | + |
| 14 | +* Nick Papior |
| 15 | +* Nils Wittemeier |
| 16 | +* Pol Febrer |
| 17 | +* Thomas Frederiksen |
| 18 | + |
| 19 | +Pull requests merged |
| 20 | +==================== |
| 21 | + |
| 22 | +A total of 30 pull requests were merged for this release. |
| 23 | + |
| 24 | +* #421: Function to build heteroribbons |
| 25 | +* #476: Refactoring the viz module to a more modular design. |
| 26 | +* #528: bug: outSile.read_scf was not able to read unconverged SCF loops |
| 27 | +* #531: enh: Added Nodes and Workflows. |
| 28 | +* #533: bug: functions could not overwrite node arguments |
| 29 | +* #534: Add env variable to docs build |
| 30 | +* #540: bug: fixed swapaxes handling |
| 31 | +* #542: mnt: changed only= keyword arguments to what= |
| 32 | +* #544: aniSileSiesta |
| 33 | +* #546: mnt: added geometry collection with some more features |
| 34 | +* #547: mnt: nodes context settings are no longer a regular input |
| 35 | +* #549: Bugfix for rotate(..., atoms=list) + additional tests |
| 36 | +* #550: changed SuperCell to Lattice, long overdue |
| 37 | +* #562: Wrap fortran files import in try/except block. |
| 38 | +* #563: Scikit build core |
| 39 | +* #566: Make documentation tabs more visual |
| 40 | +* #573: VASP forces from OUTCAR |
| 41 | +* #575: cleaned the procedure for locating maxR |
| 42 | +* #581: undo change of filenames |
| 43 | +* #585: `translate2uc` for sparse matrices with associated geometries. |
| 44 | +* #586: Slicing IO read_ routines |
| 45 | +* #589: removed Collection + GeometryCollection |
| 46 | +* #594: Fix missing import in siesta_grid. |
| 47 | +* #596: netCDF4 is now an optional dependency |
| 48 | +* #598: maint: Adapt to breaking changes in scipy.sparse.isspmatrix |
| 49 | + |
| 50 | +[0.14.0] - 2023-09-28 |
| 51 | +---------------------- |
| 52 | + |
| 53 | +Added |
| 54 | +^^^^^^ |
| 55 | +* added SISL_UNIT_SIESTA to select between legacy or codata2018 units (since Siesta 5) |
| 56 | + New default is codata2018, may create inconsistencies until Siesta 5 is widely adopted. |
| 57 | +* added --remove to sgeom for removing single atoms |
| 58 | +* added a EllipticalCylinder as a new shape |
| 59 | +* added basis-enthalpy to the stdoutSiestaSile.read_energy routine |
| 60 | +* added `read_trajectory` to read cell vectors, atomic positions, and forces from VASP OUTCAR |
| 61 | +* slicing io files multiple output (still WIP), see #584 for details |
| 62 | + Intention is to have all methods use this method for returning |
| 63 | + multiple values, it should streamline the API. |
| 64 | +* allowed xyz files to read Origin entries in the comment field |
| 65 | +* allowed sile specifiers to be more explicit: |
| 66 | + * "hello.xyz{contains=<name>}" equivalent to "hello.xyz{<name>}" |
| 67 | + * "hello.xyz{startswith=<name>}" class name should start with `<name>` |
| 68 | + * "hello.xyz{endswith=<name>}" class name should end with `<name>` |
| 69 | + This is useful for defining a currently working code: |
| 70 | + |
| 71 | + SISL_IO_DEFAULT=siesta |
| 72 | + |
| 73 | +* added environment variable ``SISL_IO_DEFAULT`` which appends a sile specifier |
| 74 | + if not explicitly added. I.e. ``get_sile("hello.xyz")`` is equivalent to |
| 75 | + ``get_sile("hello.xyz{os.environ["SISL_IO_DEFAULT"]}"``. |
| 76 | + Fixes #576 |
| 77 | +* added a context manager for manipulating the global env-vars in temporary |
| 78 | + locations. ``with sisl_environ(SISL_IO_DEFAULT=...)`` |
| 79 | +* enabled `Geometry.append|prepend` in `sgeom` command (reads other files) |
| 80 | +* added `fdfSileSiesta.write_brillouinzone` to easily write BandLines to the fdf output, |
| 81 | + see #141 |
| 82 | +* added `aniSileSiesta` for MD output of Siesta, #544 |
| 83 | +* `mdSileOpenMX` for MD output of OpenMX |
| 84 | +* `Atoms.formula` to get a chemical formula, currently only Hill notation |
| 85 | +* unified the index argument for reading Grids, `read_grid`, this influences |
| 86 | + Siesta and VASP grid reads. |
| 87 | +* `sisl.mixing`: |
| 88 | + * `AndersonMixer` enables the popular and very simple linear-like mixer |
| 89 | + * `StepMixer` allows switching between different mixers, for instance this |
| 90 | + enabled restart capabilities among other things. |
| 91 | + * Enabled composite mixers (simple math with mixers) |
| 92 | +* `BrillouinZone.merge` allows simple merging of several objects, #537 |
| 93 | + |
| 94 | +Changed |
| 95 | +^^^^^^^^ |
| 96 | +* updated the viz module, #476 |
| 97 | +* allowing ^ negation in order arguments for siles |
| 98 | +* internal change to comply with scipy changes, use issparse instead |
| 99 | + of spmatrix, see #598 |
| 100 | +* netCDF4 is now an optional dependency, #595 |
| 101 | +* interface for Sparse*.nonzero(), arguments suffixed with 's' |
| 102 | +* `stdoutSileVASP` will not accept `all=` arguments |
| 103 | +* `stdoutSileVASP.read_energy` returns as default the next item (no longer the last) |
| 104 | +* `txtSileOrca` will not accept `all=` arguments, see #584 |
| 105 | +* `stdoutSileOrca` will not accept `all=` arguments, see #584 |
| 106 | +* `xyzSile` out from sisl will now default to the extended xyz file-format |
| 107 | + Explicitly adding the nsc= value makes it compatible with other exyz |
| 108 | + file formats and parseable by sisl, this is an internal change |
| 109 | +* default of `Geometry.translate2uc`, now only periodic axes are |
| 110 | + default to be moved |
| 111 | +* all out files have been renamed to stdout to clarify they are |
| 112 | + user determined output file names, suggestion by @tfrederiksen |
| 113 | +* bumped Python requirement to >=3.8 |
| 114 | +* orbitals `R` arguments will now by default determine the minimal radii |
| 115 | + that contains 99.99% of the function integrand. The argument now |
| 116 | + accepts values -1:0 which is a fraction of the integrand that the function |
| 117 | + should contain, a positive value will explicitly set the range #574 |
| 118 | +* Added printout of the removed couplings in the `RecursiveSI` |
| 119 | +* `SuperCell` class is officially deprecated in favor of `Lattice`, see #95 for details |
| 120 | + The old class will still be accessible and usable for some time (at least a year) |
| 121 | +* Enabled EigenState.wavefunction(grid) to accept grid as the initialization of |
| 122 | + the grid argument, so one does not need to produce the `Grid` on before-hand |
| 123 | +* ``Geometry.rotate(only=)`` to ``(what=)``, this is to unify the interfaces across, #541 |
| 124 | + Also changed the default value to be "xyz" if atoms is Not none |
| 125 | +* ``tbtncSileTBtrans(only=)`` arguments are changed to (what=) #541 |
| 126 | +* `SelfEnergy.scattering_matrix` is changed to `SelfEnergy.broadening_matrix` |
| 127 | + ince the scattering matrix is an S-matrix usage. |
| 128 | + Also changed `se2scat` to `se2broadening` #529 |
| 129 | +* allow `BrillouinZone` initialization with scalar weights for all k-points #537 |
| 130 | +* `Geometry.swapaxes` and `SuperCell.swapaxes`, these are now more versatile by |
| 131 | + allowing multiple swaps in a single run, #539 |
| 132 | +* deprecated `set_sc` |
| 133 | +* internal build-system is changed to `scikit-build-core`, the `distutils` will be |
| 134 | + deprecated in Python>=3.12 so it was a needed change. |
| 135 | + This resulted in a directory restructuring. |
| 136 | + |
| 137 | + |
| 138 | +Fixed |
| 139 | +^^^^^^ |
| 140 | +* fixed Mulliken calculations for polarized calculations due to missing copy, #611 |
| 141 | +* fixed single argument `ret_isc=True` of `close`, #604 and #605 |
| 142 | +* tiling Grid now only possible for commensurate grids (grid.lattice % grid.geometry.lattice) |
| 143 | +* rare cases for non-Gamma calculations with actual Gamma matrices resulted |
| 144 | + in crashes #572 |
| 145 | +* `MonkhorstPack.replace` now checks for symmetry k-points if the BZ is using |
| 146 | + trs. Additionally the displacements are moved to the primitive point before |
| 147 | + comparing, this partly fixed #568 |
| 148 | +* spin-orbit Hamiltonians in `RealSpaceSE` and `RealSpaceSI`, fixes #567 |
| 149 | +* ufunc reductions on `SparseGeometry` where `axis` arguments reduces |
| 150 | + dimensionality |
| 151 | +* interaction with pymatgen |
| 152 | +* `fdfSileSiesta.includes` would fail when empty lines were present, #555 |
| 153 | + fixed and added test |
| 154 | +* Documentation now uses global references |
| 155 | +* `Geometry.swapaxes` would not swap latticevector cartesian coordinates, #539 |
| 156 | + |
| 157 | + |
| 158 | +toolbox.btd |
| 159 | +^^^^^^^^^^^^ |
| 160 | +# Added |
| 161 | +^^^^^^^^ |
| 162 | +* calculation of scattering matrices |
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