Released 13 of August 2024.

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 92 pull requests were merged for this release.

• #393: Linear and efficient neighbour finder
• #496: Calculate psi values on a sparse grid, to accelerate multiple...
• #497: mnt: changed spin_squared name to other name
• #647: Added a node to keep track of files
• #651: added typing hints for Lattice and LatticeChild
• #652: added sanitize to SparseCSR and setitem
• #658: Bump pypa/gh-action-pypi-publish from 1.8.10 to 1.8.11
• #659: Bump JamesIves/github-pages-deploy-action from 4.4.3 to 4.5.0
• #660: Bump actions/setup-python from 4 to 5
• #662: Bump github/codeql-action from 2 to 3
• #663: Bump actions/upload-artifact from 3 to 4
• #664: Bump actions/download-artifact from 3 to 4
• #665: moving towards functional programming in sisl
• #666: Support for conditional expressions on workflows.
• #667: ensure that workflows have (and transmit) the right state
• #668: WIP: Added a matrix plot
• #670: Missing fdf flags error
• #672: first try at implementing bond-order calculations
• #673: removed selector from code base
• #679: Bump codecov/codecov-action from 3 to 4
• #681: Fix multisize 3D balls in plots
• #682: Added Jmol colors as defaults for atoms.
• #683: Added pre-commit config
• #684: Some tweaks to atom colors
• #686: 579 dftb hamiltonian
• #692: Lazy loading of the viz module
• #693: Fix wheels workflow
• #695: added typing in lots of io places, added SileSlicer
• #696: Bump pypa/gh-action-pypi-publish from 1.8.11 to 1.8.12
• #697: Optimize nsc after reading Hamiltonian from wann90 output
• #702: fixed #700 by reverting 7cf88f1a5
• #704: Bump pypa/gh-action-pypi-publish from 1.8.12 to 1.8.14
• #706: cleaned finder and removed pbc (getting it from Lattice)
• #710: removed txtSileOrca.no/info.no since it was never present
• #711: added warning for complex grids and isosurface
• #714: 675 documentation
• #715: Bump pypa/cibuildwheel from 2.16 to 2.17
• #717: Fix for reading spinful CHG/CHGCAR
• #722: Add read_gtensor and read_hyperfine_coupling to txtSileORCA
• #723: add test for reading Hamiltonian from wannier90 output
• #725: Additional energy units
• #726: units as parameter in read_*
• #727: Resolve Issue #716
• #729: Minor ORCA/VASP documentation improvements
• #734: Remove deprecated bc argument to Grid
• #736: Some polishing of sisl.nodes
• #737: added math notation convention
• #739: Ensure module is fine on node class creation
• #742: Draft: add vectorsSileSIESTA for parsing vibra output
• #743: Added specific functions to create animations and subplots
• #746: 745 rtd files
• #749: Ensure c-order for Geometry coordinates
• #750: norm2 as atom-resolved quantity
• #751: made State.inner a very flexible matrix product
• #752: added hexagonal and goldene
• #753: removed sisl.plot from the code base
• #754: Reading spin densities from CHGCAR
• #755: Bump JamesIves/github-pages-deploy-action from 4.5.0 to 4.6.0
• #757: Plot update on getting attributes
• #758: Added declaration of some attributes in Figure
• #759: Removed nodes from sisl
• #761: removed 3.8 support, bumped min to 3.9
• #762: CI also run on minimal installation
• #763: changed phonon displacement shape
• #765: Modifying the returns of the neighbor finder
• #767: fixed pbc usage across sisl, fixes #764
• #769: Bump pypa/cibuildwheel from 2.17 to 2.18
• #771: Removed leftover print
• #772: Removed deprecated argument diag->projection
• #773: Dihedral angles
• #774: Bump JamesIves/github-pages-deploy-action from 4.6.0 to 4.6.1
• #776: Add support for sisl in nodify's GUI
• #779: fixed reading geometries from fdf + XV + STRUCT
• #780: Allow dash to be set in bands plots.
• #781: Allow tuning matplotlib subplots.
• #784: Legend grouping in bands plots
• #786: Allow custom color scales across sisl.viz
• #787: Clarify viz dependencies error
• #788: Bump pypa/cibuildwheel from 2.18 to 2.19
• #789: Bump pypa/gh-action-pypi-publish from 1.8.14 to 1.9.0
• #790: fixed lots of parallel calculations
• #792: trying to remove numpy 2 (as a temporary work-around)
• #793: adding test for parallel calculation
• #796: Clarify out of memory error on density
• #797: 766 shc
• #803: Bump JamesIves/github-pages-deploy-action from 4.6.1 to 4.6.3
• #804: ensured building against numpy>=2
• #805: Fix bug with numpy v2.0
• #807: Fix fatbands with negative size
• #809: enabled vacuum for all geometries with non-pbc directions
• #812: completed tests rearrangement
• #818: fixing many simple PEP-585 deprecations

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, #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, #750

• improved typing system

• units to read_* for some Siles, #726

• enabled reading the Hamiltonian from the Wannier90 _tb.dat file, #727

• "Hz", "MHz", "GHz", "THz", and "invcm" as valid energy units, #725

• added read_gtensor and read_hyperfine_coupling to txtSileORCA, #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, #393

• enabled reading DFTB+ output Hamiltonian and overlap matrices, #579

• bond_order for DensityMatrix objects, #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, #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, #668

Fixed

• PEP-585 compliant
• buildable for numpy>2, #791
• BrillouinZone.tocartesian() now defaults to k=self.k
• reading XV/STRUCT files from fdf siles could cause problems, #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, #764
• fixed CHGCAR spin-polarized density reads, #754
• dispatch methods now searches the mro for best matches, #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, #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, #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 #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, #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, #640
• documentation build system on RTD is updated, #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, #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 #586 for details
• AtomNeighbours changed name to AtomNeighbor to follow #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.