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@@ -30,6 +30,7 @@ Changelogs | |
| .. toctree:: | ||
| :maxdepth: 1 | ||
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| v0.15.0 | ||
| v0.14.3 | ||
| v0.14.2 | ||
| v0.14.0 | ||
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| Original file line number | Diff line number | Diff line change |
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| ****** | ||
| 0.15.0 | ||
| ****** | ||
|
|
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| Released 13 of August 2024. | ||
|
|
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| Contributors | ||
| ============ | ||
|
|
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| A total of 4 people contributed to this release. People with a "+" by their | ||
| names contributed a patch for the first time. | ||
|
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| * Nick Papior | ||
| * Nils Wittemeier | ||
| * Pol Febrer | ||
| * Thomas Frederiksen | ||
|
|
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| Pull requests merged | ||
| ==================== | ||
|
|
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| A total of 92 pull requests were merged for this release. | ||
|
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| * :pull:`#393 <393>`: Linear and efficient neighbour finder | ||
| * :pull:`#496 <496>`: Calculate psi values on a sparse grid, to accelerate multiple... | ||
| * :pull:`#497 <497>`: mnt: changed spin_squared name to other name | ||
| * :pull:`#647 <647>`: Added a node to keep track of files | ||
| * :pull:`#651 <651>`: added typing hints for Lattice and LatticeChild | ||
| * :pull:`#652 <652>`: added sanitize to SparseCSR and __setitem__ | ||
| * :pull:`#658 <658>`: Bump pypa/gh-action-pypi-publish from 1.8.10 to 1.8.11 | ||
| * :pull:`#659 <659>`: Bump JamesIves/github-pages-deploy-action from 4.4.3 to 4.5.0 | ||
| * :pull:`#660 <660>`: Bump actions/setup-python from 4 to 5 | ||
| * :pull:`#662 <662>`: Bump github/codeql-action from 2 to 3 | ||
| * :pull:`#663 <663>`: Bump actions/upload-artifact from 3 to 4 | ||
| * :pull:`#664 <664>`: Bump actions/download-artifact from 3 to 4 | ||
| * :pull:`#665 <665>`: moving towards functional programming in sisl | ||
| * :pull:`#666 <666>`: Support for conditional expressions on workflows. | ||
| * :pull:`#667 <667>`: ensure that workflows have (and transmit) the right state | ||
| * :pull:`#668 <668>`: WIP: Added a matrix plot | ||
| * :pull:`#670 <670>`: Missing fdf flags error | ||
| * :pull:`#672 <672>`: first try at implementing bond-order calculations | ||
| * :pull:`#673 <673>`: removed selector from code base | ||
| * :pull:`#679 <679>`: Bump codecov/codecov-action from 3 to 4 | ||
| * :pull:`#681 <681>`: Fix multisize 3D balls in plots | ||
| * :pull:`#682 <682>`: Added Jmol colors as defaults for atoms. | ||
| * :pull:`#683 <683>`: Added pre-commit config | ||
| * :pull:`#684 <684>`: Some tweaks to atom colors | ||
| * :pull:`#686 <686>`: 579 dftb hamiltonian | ||
| * :pull:`#692 <692>`: Lazy loading of the viz module | ||
| * :pull:`#693 <693>`: Fix wheels workflow | ||
| * :pull:`#695 <695>`: added typing in lots of io places, added SileSlicer | ||
| * :pull:`#696 <696>`: Bump pypa/gh-action-pypi-publish from 1.8.11 to 1.8.12 | ||
| * :pull:`#697 <697>`: Optimize nsc after reading Hamiltonian from wann90 output | ||
| * :pull:`#702 <702>`: fixed #700 by reverting 7cf88f1a5 | ||
| * :pull:`#704 <704>`: Bump pypa/gh-action-pypi-publish from 1.8.12 to 1.8.14 | ||
| * :pull:`#706 <706>`: cleaned finder and removed pbc (getting it from Lattice) | ||
| * :pull:`#710 <710>`: removed txtSileOrca.no/info.no since it was never present | ||
| * :pull:`#711 <711>`: added warning for complex grids and isosurface | ||
| * :pull:`#714 <714>`: 675 documentation | ||
| * :pull:`#715 <715>`: Bump pypa/cibuildwheel from 2.16 to 2.17 | ||
| * :pull:`#717 <717>`: Fix for reading spinful CHG/CHGCAR | ||
| * :pull:`#722 <722>`: Add `read_gtensor` and `read_hyperfine_coupling` to `txtSileORCA` | ||
| * :pull:`#723 <723>`: add test for reading Hamiltonian from wannier90 output | ||
| * :pull:`#725 <725>`: Additional energy units | ||
| * :pull:`#726 <726>`: `units` as parameter in `read_*` | ||
| * :pull:`#727 <727>`: Resolve Issue #716 | ||
| * :pull:`#729 <729>`: Minor ORCA/VASP documentation improvements | ||
| * :pull:`#734 <734>`: Remove deprecated `bc` argument to `Grid` | ||
| * :pull:`#736 <736>`: Some polishing of `sisl.nodes` | ||
| * :pull:`#737 <737>`: added math notation convention | ||
| * :pull:`#739 <739>`: Ensure __module__ is fine on node class creation | ||
| * :pull:`#742 <742>`: Draft: add vectorsSileSIESTA for parsing vibra output | ||
| * :pull:`#743 <743>`: Added specific functions to create animations and subplots | ||
| * :pull:`#746 <746>`: 745 rtd files | ||
| * :pull:`#749 <749>`: Ensure c-order for `Geometry` coordinates | ||
| * :pull:`#750 <750>`: `norm2` as atom-resolved quantity | ||
| * :pull:`#751 <751>`: made State.inner a very flexible matrix product | ||
| * :pull:`#752 <752>`: added hexagonal and goldene | ||
| * :pull:`#753 <753>`: removed sisl.plot from the code base | ||
| * :pull:`#754 <754>`: Reading spin densities from CHGCAR | ||
| * :pull:`#755 <755>`: Bump JamesIves/github-pages-deploy-action from 4.5.0 to 4.6.0 | ||
| * :pull:`#757 <757>`: Plot update on getting attributes | ||
| * :pull:`#758 <758>`: Added declaration of some attributes in Figure | ||
| * :pull:`#759 <759>`: Removed nodes from `sisl` | ||
| * :pull:`#761 <761>`: removed 3.8 support, bumped min to 3.9 | ||
| * :pull:`#762 <762>`: CI also run on minimal installation | ||
| * :pull:`#763 <763>`: changed phonon displacement shape | ||
| * :pull:`#765 <765>`: Modifying the returns of the neighbor finder | ||
| * :pull:`#767 <767>`: fixed pbc usage across sisl, fixes #764 | ||
| * :pull:`#769 <769>`: Bump pypa/cibuildwheel from 2.17 to 2.18 | ||
| * :pull:`#771 <771>`: Removed leftover print | ||
| * :pull:`#772 <772>`: Removed deprecated argument `diag->projection` | ||
| * :pull:`#773 <773>`: Dihedral angles | ||
| * :pull:`#774 <774>`: Bump JamesIves/github-pages-deploy-action from 4.6.0 to 4.6.1 | ||
| * :pull:`#776 <776>`: Add support for sisl in nodify's GUI | ||
| * :pull:`#779 <779>`: fixed reading geometries from fdf + XV + STRUCT | ||
| * :pull:`#780 <780>`: Allow dash to be set in bands plots. | ||
| * :pull:`#781 <781>`: Allow tuning matplotlib subplots. | ||
| * :pull:`#784 <784>`: Legend grouping in bands plots | ||
| * :pull:`#786 <786>`: Allow custom color scales across sisl.viz | ||
| * :pull:`#787 <787>`: Clarify viz dependencies error | ||
| * :pull:`#788 <788>`: Bump pypa/cibuildwheel from 2.18 to 2.19 | ||
| * :pull:`#789 <789>`: Bump pypa/gh-action-pypi-publish from 1.8.14 to 1.9.0 | ||
| * :pull:`#790 <790>`: fixed lots of parallel calculations | ||
| * :pull:`#792 <792>`: trying to remove numpy 2 (as a temporary work-around) | ||
| * :pull:`#793 <793>`: adding test for parallel calculation | ||
| * :pull:`#796 <796>`: Clarify out of memory error on density | ||
| * :pull:`#797 <797>`: 766 shc | ||
| * :pull:`#803 <803>`: Bump JamesIves/github-pages-deploy-action from 4.6.1 to 4.6.3 | ||
| * :pull:`#804 <804>`: ensured building against numpy>=2 | ||
| * :pull:`#805 <805>`: Fix bug with numpy v2.0 | ||
| * :pull:`#807 <807>`: Fix fatbands with negative size | ||
| * :pull:`#809 <809>`: enabled vacuum for all geometries with non-pbc directions | ||
| * :pull:`#812 <812>`: completed tests rearrangement | ||
| * :pull:`#818 <818>`: fixing many simple PEP-585 deprecations | ||
|
|
||
| [0.15.0] - 2024-08-13 | ||
| --------------------- | ||
|
|
||
| Added | ||
| ^^^^^ | ||
| * conversion of list-like elements to `Lattice` | ||
| * vacuum argument for all `sisl.geom` methods that can use it | ||
| * `Geometry.find_nsc`, alternate method for calculating `nsc` with more options | ||
| * `sisl._debug_info` for more complete debug information | ||
| * `axes` argument added to `derivative` to only calculate on a subset | ||
| of directions (can greatly improve performance for some systems) | ||
| * `operator` argument added to `derivative` to apply an operator | ||
| to `dHk` and `dSk` matrices. | ||
| of directions (can greatly improve performance for some systems) | ||
| * added `apply_kwargs` to methods which uses a `BrillouinZone` object. | ||
| This enables one to leverage parallel processing for calculations. | ||
| * `SISL_PAR_CHUNKSIZE=25`, new default parameter for parallel processing. | ||
| Can greatly improve parallel processing of BZ integrations | ||
| * added `vectorsSileSiesta` to read vibra eigenmode output | ||
| * added `dihedral` to `Geometry`, :pull:`#773 <773>` | ||
| * ability to retain sub-classes through `<class>.new` calls | ||
| * added `Listify` to ensure arguments behaves as *iterables* | ||
| * setter for `Lattice.pbc` to specify it through an array | ||
| * `Lattice.volumef` to calculate a subset volume based on axes | ||
| * added `write_grid` to Siesta binary grid files | ||
| * added the `goldene` 2D lattice, a `hexagonal` Gold 2D structure | ||
| * added the `hexagonal` 2D lattice, close-packed FCC(111) surface | ||
| * improved `atom` projections of states, :pull:`#750 <750>` | ||
| * improved typing system | ||
| * `units` to `read_*` for some `Sile`s, :pull:`#726 <726>` | ||
| * enabled reading the Hamiltonian from the Wannier90 _tb.dat file, :pull:`#727 <727>` | ||
| * "Hz", "MHz", "GHz", "THz", and "invcm" as valid energy units, :pull:`#725 <725>` | ||
| * added `read_gtensor` and `read_hyperfine_coupling` to `txtSileORCA`, :pull:`#722 <722>` | ||
| * enabled `AtomsArgument` and `OrbitalsArgument` to accept `bool` for *all* or *none* | ||
| * enabled `winSileWannier90.read_hamiltonian` to read the ``_tb.dat`` files | ||
| * `atoms` argument to `DensityMatrix.spin_align` to align a subset of atoms | ||
| (only diagonal elements between the atoms orbitals) | ||
| * added an efficient neighbor finder, :pull:`#393 <393>` | ||
| * enabled reading DFTB+ output Hamiltonian and overlap matrices, :pull:`#579 <579>` | ||
| * `bond_order` for `DensityMatrix` objects, :pull:`#507 <507>` | ||
| * better error messages when users request quantities not calculated by Siesta/TBtrans | ||
| * functional programming of the basic sisl classes | ||
| Now many of the `Geometry|Lattice|Grid.* manipulation routines which | ||
| returns new objects, are subjected to dispatch methods. | ||
| E.g. | ||
|
|
||
| sisl.tile(geometry, 2, axis=1) | ||
| geometry.tile(2, axis=1) | ||
|
|
||
| will call the same method. The first uses a dispatch method, and a `SislError` | ||
| will be raised if the dispatch argument is not implemented. | ||
| * `SparseCSR.toarray` to comply with array handling (equivalent to `todense`) | ||
| * enabled `Grid.to|new` with the most basic stuff | ||
| str|Path|Grid|pyamg | ||
| * `Shape.translate`, to easily translate entire shape constructs, :pull:`#655 <655>` | ||
| * Creation of chiral GNRs (`kind=chiral` in `sisl.geom.nanoribbon`/`sisl.geom.graphene_nanoribbon` | ||
| as well as `sisl.geom.cgnr`) | ||
| * Creation of [n]-triangulenes (`sisl.geom.triangulene`) | ||
| * added `offset` argument in `Geometry.add_vacuum` to enable shifting atomic coordinates | ||
| * A new `AtomicMatrixPlot` to plot sparse matrices, :pull:`#668 <668>` | ||
|
|
||
| Fixed | ||
| ^^^^^ | ||
| * PEP-585 compliant | ||
| * buildable for numpy>2, :pull:`#791 <791>` | ||
| * `BrillouinZone.tocartesian()` now defaults to `k=self.k` | ||
| * reading XV/STRUCT files from fdf siles could cause problems, :pull:`#778 <778>` | ||
| * `Geometry.[ao][us]c2[su]c` methods now retains the input shapes (unless `unique=True`) | ||
| * lots of `Lattice` methods did not consistently copy over BC | ||
| * `BrillouinZone.volume` fixed to actually return BZ volume | ||
| use `Lattice.volume` for getting the lattice volume. | ||
| * xsf files now only respect `lattice.pbc` for determining PBC, :pull:`#764 <764>` | ||
| * fixed `CHGCAR` spin-polarized density reads, :pull:`#754 <754>` | ||
| * dispatch methods now searches the mro for best matches, :pull:`#721 <721>` | ||
| * all `eps` arguments has changed to `atol` | ||
| * methods with `axis` arguments now accepts the str equivalent 0==a | ||
| * documentation links to external resources | ||
| * fixed `chgSileVASP.read_grid` for spinful calculations | ||
| * `txtSileOrca.info.no` used a wrong regex, added a test | ||
| * raises error when requesting isosurface for complex valued grids, :pull:`#709 <709>` | ||
| * some attributes associated with `Sile.info.*` will now warn instead of raising information | ||
| * reading matrices from HSX files with *weird* labels, should now work (*fingers-crossed*) | ||
| * `Atom(Z="1000")` will now correctly work, :pull:`#708 <708>` | ||
| * `AtomUnknown` now also has a default mass of 1e40 | ||
| * changed `read_force_constant` to `read_hessian`, the old methods are retained with | ||
| deprecation warnings. | ||
| * `pdosSileSiesta` plotting produced wrong spin components for NC/SOC | ||
| * `tqdm` changed API in 2019, `eta=True` in Notebooks should now work | ||
| * `SparseCSR` ufunc handling, in some corner cases could the dtype casting do things | ||
| wrongly. | ||
| * fixed corner cases where the `SparseCSR.diags(offsets=)` would add elements | ||
| in non-existing elements | ||
| * some cases of writing orthogonal matrices to TSHS/nc file formats :pull:`#661 <661>` | ||
| * `BDOS` from TBtrans calculations now returns the full DOS of all (Bloch-expanded) | ||
| atoms | ||
| * `Lattice` objects now issues a warning when created with 0-length vectors | ||
| * HSX file reads should respect input geometry arguments | ||
| * enabled slicing in matrix assignments, :pull:`#650 <650>` | ||
| * changed `Shape.volume()` to `Shape.volume` | ||
| * growth direction for zigzag heteroribbons | ||
| * `BandStructure` points can now automatically add the `nsc == 1` axis as would | ||
| be done for assigning matrix elements (it fills with 0's). | ||
|
|
||
| Removed | ||
| ^^^^^^^ | ||
| * `degenerate` argument in `velocity`/`derivative`, they do not belong there | ||
| * `xvSileSiesta.read_geometry(species_as_Z)`, deprecated in favor of `atoms=` | ||
| * `structSileSiesta.read_geometry(species_as_Z)`, deprecated in favor of `atoms=` | ||
| * `Atom.radii` is removed, `Atom.radius` is the correct invocation | ||
| * `sisl.plot` is removed (`sisl.viz` is replacing it!) | ||
| * `cell` argument for `Geometry.translate/move` (it never worked) | ||
| * removed `Selector` and `TimeSelector`, they were never used internally | ||
|
|
||
| Changed | ||
| ^^^^^^^ | ||
| * internal test structure, should improve future progress | ||
| * `Lattice.parameters` now returns a 2-tuple of ``length, angles`` | ||
| * units of `conductivity` has changed to S / Ang | ||
| * `conductivity` is deprecated, use `ahc` and `shc` instead | ||
| * `berry_curvature` has completely changed, checks it API | ||
| * BZ apply methods are now by default parallel (if ``SISL_NUM_PROCS>1``) | ||
| * `hsxSileSiesta.read_hamiltonian` now implicitly shifts Fermi-level to 0 (for newer HSX versions) | ||
| * deprecated `periodic` to `axes` argument in `BrillouinZone.volume` | ||
| * changed `Eigenmode.displacement` shape, please read the documentation | ||
| * bumped minimal Python version to 3.9, :pull:`#640 <640>` | ||
| * documentation build system on RTD is updated, :pull:`#745 <745>` | ||
| * `gauge` arguments now accept 'cell' and 'orbital' in replacements for 'R' and 'r', respectively | ||
| * `siesta.*.read_basis` now defaults to read an `Atoms` object with all atoms | ||
| * `atoms.specie` changed to `atoms.species`, generally species is the singular form | ||
| * `in_place` arguments changed to `inplace` | ||
| * renamed `stdoutSileVASP` to `outcarSileVASP`, :pull:`#719 <719>` | ||
| * deprecated scale_atoms in favor of scale_basis in `Geometry.scale` | ||
| * changed default number of eigenvalues calculated in sparse `eigsh`, from 10 to 1 | ||
| * `stdoutSileSiesta.read_*` now defaults to read the *next* entry, and not the last | ||
| * `stdoutSileSiesta.read_*` changed MD output functionality, see :pull:`#586 <586>` for details | ||
| * `AtomNeighbours` changed name to `AtomNeighbor` to follow :pull:`#393 <393>` | ||
| * changed method name `spin_squared` to `spin_contamination` | ||
| * removed `Lattice.translate|move`, they did not make sense, and so their | ||
| usage should be deferred to `Lattice.add` instead. | ||
| * `vacuum` is now an optional parameter for all ribbon structures | ||
| * enabled `array_fill_repeat` with custom axis, to tile along specific | ||
| dimensions | ||
| * Importing `sisl.viz` explicitly is no longer needed, as it will be lazily | ||
| loaded whenever it is required. |
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