v0.15.2

Released 6 of November 2024.

Contributors

A total of 3 people contributed to this release. People with a "+" by their
names contributed a patch for the first time.

• Arnold Kole +
• Nick Papior
• Pol Febrer

Pull requests merged

A total of 14 pull requests were merged for this release.

• #691: Parsing of Mulliken charges from SIESTA stdout
• #833: Fixed spin polarized fatbands
• #836: Fix orbital values when an orbital is completely outside of the unit cell
• #843: Fix sparse grid tests
• #844: Fix failing test for minimal dependencies
• #845: Accessors and grouping documentation entries
• #846: fixed bug reading geometry from ncSileSiesta
• #848: Allow for any type of integer when requesting neighbor items
• #849: Improve plotables documentation
• #850: trying to fix the within_inf problem
• #851: major restructure of the documentation
• #857: fixed 5.2 reading of charges
• #859: Use cutoff from basis files (xml, nc)
• #860: New wheels

Maintenance pull requests merged

A total of 4 pull requests were merged for this release.

• #830: Bump pypa/gh-action-pypi-publish from 1.10.1 to 1.10.2
• #834: Bump JamesIves/github-pages-deploy-action from 4.6.4 to 4.6.8
• #837: Bump pypa/gh-action-pypi-publish from 1.10.2 to 1.10.3
• #855: Bump pypa/gh-action-pypi-publish from 1.10.3 to 1.11.0

Changelog

Added

• added timesSileSiesta which can read siesta TIMES output
• Parsing of total Mulliken charges in stdoutSileSiesta, #691

Fixed

• reading charges from Siesta 5.2 output files, #856
• a read problem for very big simulations (related to orbindxSileSiesta)
• bug-fix for tbtSileTBtrans.Eindex handling of integers, #829
  This is a regression fix, integers will now be handled differently
  than prior releases.
  A warning is raised to inform users.
• fixed warning raised when reading electronic structure without Ef, #826
• fixed precision writing of energies in GF files (siesta), #827
• fixed reading HSetupOnly HSX files from Siesta, #828
• fixed reading stresses and forces from stdoutSileSiesta
  Note that generally the forces/stresses in the Final section of the
  output will not be returned. Only if there are no other forces/stresses
  in the output file.

Changed

• tbtSileTBtrans.Eindex changed, see #829 for details.

v0.15.1

Released 10 of September 2024.

Contributors

A total of 2 people contributed to this release. People with a "+" by their
names contributed a patch for the first time.

• Nick Papior
• Pol Febrer

Pull requests merged

A total of 5 pull requests were merged for this release.

• #819: Make sure wheels are uploaded to pypi
• #822: Bump pypa/gh-action-pypi-publish from 1.9.0 to 1.10.0
• #823: Fix orbital values
• #824: Bump pypa/gh-action-pypi-publish from 1.10.0 to 1.10.1
• #825: Bump JamesIves/github-pages-deploy-action from 4.6.3 to 4.6.4

Added

• enabled lowdin to return the Lowdin transformation matrix, and also
  allow it to be calculated using SVD

Fixed

• bugfix for wrong call Lattice.to.cuboid which caused wrong densities, #821

v0.15.0

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 7cf88f1
• #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)
  ...

v0.14.3

Released 7 of November 2023.

Contributors

A total of 2 people contributed to this release. People with a "+" by their
names contributed a patch for the first time.

• Nick Papior
• Pol Febrer

Pull requests merged

A total of 11 pull requests were merged for this release.

• #627: Update DEPLOY.md with pyodide instructions
• #628: maint: allow stopping traversal of node trees
• #629: Lattice is now owning the boundary conditions
• #630: Included missing notebook in the viz docs
• #631: Added Info attributes to ascii class files
• #634: fixed #633 due to weird combination of boundary lookups
• #635: added an as_supercell which returns geometry in supercell
• #636: Honeycomb flakes
• #637: Optionally avoid custom node errors.
• #639: Black linting
• #642: Deprecated xarray argument

[0.14.3] - 2023-11-07

Added

• Creation of honeycomb flakes (sisl.geom.honeycomb_flake,
  sisl.geom.graphene_flake). #636
• added Geometry.as_supercell to create the supercell structure,
  thanks to @pfebrer for the suggestion
• added Lattice.to and Lattice.new to function the same
  as Geometry, added Lattice.to["Cuboid"]
• added Atom.to, currently only to.Sphere()
• enabled Geometry.to|new.Sile(...)
• added logging in some modules, to be added in more stuff to allow easier
  debugging.
• marked all toSphere|toEllipsoid|... as deprecated
• a simple extensionable method to add Sile.info.<attr> by exposing
  attributes through an object on each class.
  The info_attributes contains a list of attributes that can be
  discovered while reading ascii files see #509

Fixed

• fixed cases where Geometry.close would not catch all neighbours, #633

Changed

• sisl now enforces the black style
• Lattice now holds the boundary conditions (not Grid), see #626
• Some siles exposed certain properties containing basic information
  about the content, say number of atoms/orbitals etc.
  These will be moved to sile.info.<attr> instead to reduce
  the number of methods exposed on each sile.

v0.14.2

Released 4 of October 2023.

Contributors

A total of 2 people contributed to this release. People with a "+" by their
names contributed a patch for the first time.

• Nick Papior
• Pol Febrer

Pull requests merged

A total of 5 pull requests were merged for this release.

• #619: Some fixes in sisl.viz
• #620: bug: register data classes as plotables
• #621: Cleaning tutorial notebooks.
• #623: bug: introduction of meta attribute broke heatmaps
• #624: bug: origin not properly preserved during grid plotting

[0.14.2] - 2023-10-04

Fixed

• problems in the sisl.viz module got fixed

Changed

• xarray is now a full dependency (this also implies pandas)

v0.14.0

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
• #613: Bump JamesIves/github-pages-deploy-action from 4.4.1 to 4.4.3
• #614: Bump pypa/gh-action-pypi-publish from 1.6.4 to 1.8.10
• #615: Bump actions/checkout from 3 to 4
• #616: Bump pypa/cibuildwheel from 2.15 to 2.16
• #617: Bump pypa/gh-action-pypi-publish from 1.6.4 to 1.8.10

[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=}" equivalent to "hello.xyz{}"

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

  • "hello.xyz{endswith=}" 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

v0.13.0

Released 18 of January 2023.

Contributors

A total of 5 people contributed to this release. People with a "+" by their
names contributed a patch for the first time.

• A.H. Kole
• Nick Papior
• Nils Wittemeier +
• Pol Febrer
• Thomas Frederiksen

Pull requests merged

A total of 18 pull requests were merged for this release.

• #487: Fix issue 486 - in correct sign of the y component of the spin...
• #489: bug: fixed #488 with the cell order
• #494: enh: enabling reading of file-handles and StringIO
• #498: 495 deprecation
• #499: Easy construction of hydrogenic orbitals
• #500: Reading output from ORCA
• #503: Plotly is incompatible with ipywidgets 8.x
• #504: Allow reading forces from transiesta in output file
• #508: New keywords in step_to()
• #510: Add CodeQL workflow for GitHub code scanning
• #511: Possible bug: within_inf with periodic=False returns sc atoms...
• #514: Surface slab geometries: clarify vacuum=None as a possibility...
• #515: doc: fixed indices in sums
• #516: mnt: changed index ordering of spin-charge quantities
• #519: Fix reading of basis
• #520: ORCA API
• #521: Minor fixes for IO-API
• #526: bug: reading the EDM from fdf did not read geometry automatically

Added

• Geometry.apply apply functions to slices of data depending on the geometry
• enabled Gaussian and Slater type orbitals, #463
  Please give feedback!
• deltancSileTBtrans.merge allowing easy merging of several delta
  siles, #513
• implemented reading of output files from ORCA, #500
• HydrogenicOrbital is added for simple handling of 1-valence electron
  orbitals, #499
• Bohr radius to constants
• enabled ASCII siles to read from file-handles and buffers, #484
• enabled unit specification for lengths in cube-files
• added kwargs passed to eigenstate functions in berry_phase
  and conductivity
• ensured that non-orthogonal transform will copy over overlap matrix
  in case the matrix is only touching the non-overlap elements
• enabled dictionary entries for the Atoms initialization
  in place of atoms argument. Both in the list-like entry, or
  as the only argument.

Fixed

• rare compiler bug, #512
• within_inf with periodic arguments, #511
• reading TranSiesta data from outSileSiesta
• regression from 80f27b0, reading version 0 HSX content, #492
• delta-files (netCDF) would always have diagonal components,
  this has now been removed since it only needs the elements with
  values
• Siesta sparse matrices could in some cases set wrong diagonal
  components
• too large energies in Siesta files could result in crash, #482
• orbital quantum numbers from HSX file was wrong in v1, #462
• corrected sign for spin-Y direction, PDOS, spin_moment, #486
• RealSpaceSI for right semi-infinite directions, #475
• tbtrans files now have a separate entry in the documentation

Changed

• removed all deprecated routines, #495
• oplist now can do in-place operations on generators
• significant performance improvement for COOP calculations,
  thanks to Susanne Leitherer for discovering the issue
• changed argument order of ElectronState.COP
• index ordering of spin and coordinate quantities are now changed to
  have these as the first indices. This ensures consistency across
  return types and allows easier handling.
  Note that non-polarized PDOS calculations now has an extra dimension
  for coherence with non-colinear spin. (see #501)
• ensured all units are now CODATA-2018 values
• cell_length changed to cell2length with new axes argument
• enabled orbitals up to the h-shell, #491
• swapped order of honeycomb (graphene derivatives)
  lattice vectors, to ensure the vectors are following right-hand-rule, #488
• changed DIIS solver to assume the matrix is symmetric (it is)
• tbtncSileTBtrans and its derivates has changed, drastically.
  This will accommodate changes related to #477 and #478.
  Now *_transmission refers to energy resolved transmissions
  and *_current reflects bias-window integrated quantities.
  The defaults and argument order has changed drastically, so
  users should adapt their scripts depending on sisl version.
  A check can be made, if sisl.__version_tuple__[:3] >= (0, 13, 0):
• To streamline argument order the *_ACO[OH]P routines have changed
  elec and E argument order. This makes them compatible with
  orbital_transmission etc.

v0.12.2

Contributors

A total of 3 people contributed to this release. People with a "+" by their
names contributed a patch for the first time.

• Nick Papior
• Pol Febrer
• Thomas Frederiksen

Pull requests merged

A total of 4 pull requests were merged for this release.

• #444: Function to translate atoms in geometry into the unit cell
• #445: Suggestions to docs
• #447: Minor things
• #451: enh: enabled PBC center of mass calculations

Added

• enabled parsing geometry.in files from FHIaims
• added batched_indices for memory-reduced location of array values
• enabled manifold extractions sisl.physics.yield_manifolds
• enabled center of mass for periodic systems (chooses best COM)
• enabled returning the overlap matrix from berry_phase
• added rocksalt @tfrederiksen
• slab geometry creations, fcc_slab, bcc_slab and rocksalt_slab @tfrederiksen
• added Geometry.translate2uc to shift everything into the unit-cell @tfrederiksen
• added Geometry.unrepeat to reverse repeat calls (and to sgeom)
• added SparseGeometry.unrepeat to reverse repeat calls

Fixed

• enabled reading HSX file version 1, #432
• major performance boost for reading GULP FC files
• cleaned mixing methods and decoupled the History and Mixers
• incorrect handling of atoms argument in Geometry.center calls

Changed

• State*.outer corrected to the same interface as State*.inner
• all sisl.geom geometries are now calling optimize_nsc if needed
• SparseGeometry.cut -> SparseGeometry.untile
  • much faster
  • many more checks to warn about wrong usage
    • cut is now deprecated (removed in 0.13)
    • changed the --cut flag in sgeom to --untile, deprecated flag
• enabled in/out arguments to tbt siles (easier to remember meaning)

v0.12.1

Contributors

A total of 2 people contributed to this release. People with a "+" by their
names contributed a patch for the first time.

• Nick Papior
• Pol Febrer

Pull requests merged

A total of 0 pull requests were merged for this release.

Added

• return spin moment from SCF output files of Siesta
• read_fermi_level to siesta.PDOS files

Fixed

• MacOS builds
• sdata handling of siesta.PDOS* files, much more versatily now
• masking import of xarray
• Fixes to sisl.viz module related to 3.10 and other details

v0.12.0

Contributors

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

• A.H. Kole +
• Nick Papior
• Pol Febrer
• Thomas Frederiksen

Pull requests merged

A total of 14 pull requests were merged for this release.

• #307 : Reading net charges from outSileSiesta
• #313 : doc: added description of dictionary keys and fixed a typo
• #365 : mnt: changed all origo references to origin
• #367 : Parallel calculation of PDOS and (fat)bands
• #368 : Allow per-category atom styles in GeometryPlot
• #371 : bug: fixed some errors in tutorial notebooks
• #374 : bug: geometry plot tests were failing
• #376 : tests: removed plotly requirement to test sisl.viz
• #378 : mnt: fixed matplotlib tests in <=3.4
• #382 : bug: 2D geometry plots didn't take perspective into account.
• #395 : Quick bug fix. Plot was not callable.
• #397 : tests: avoid too many matplotlib figures
• #402 : Use PeriodicTable to convert atomic labels to atomic numbers...
• #403 : Fixed construction of non-orthogonal (2-atom) hcp cell

Added

• Geometry.sub_orbital is added
• BrillouinZone.volume enables easy calculation of volumes for BZ integrals
• State.sub|remove are now allowed to be done inplace
• State.derivative can now correctly calculate 1st and 2nd order derivatives #406
• Enabled discontinuity jumps in band-structures (pass points as None)
• COOP and COHP calculations for eigenstates
• inverse participation ration calculations (with arbitrary q)
• origin point for mirror functionality (Geometry)
• degenerate_dir for velocity directions
• State.remove complementary to State.sub
• copying Dispatchers for subclasses.
• dispatchers to Shape
• Spin.spinor to get number of spinor components
• sc argument to xyzSile.read_geometry for user defined cells
• tiling a State object, #354 and #355
• replacing atoms in SparseOrbital geometries #139
• direction now accepts abc and xyz keywords to retrieve vectors depending on direction input.
• replacing atoms in SparseOrbital geometries #139
• reading from STRUCT_* files (Siesta input/output) #308
• reading the SuperCell block from fdf
• reading PAO.Basis blocks from both out and fdf files, almost complete functionality #90
• generic transform method for matrix transformations
• doing ufunc.reduce on SparseCSR matrices; wrong values for e.g. np.prod, generally be CAUTIOUS with reduction operations
• transposing a SparseCSR matrix
• added pymatgen conversion (Geometry.to/from.pymatgen)
• atom indexing by shapes #337

Fixed

• sub_orbital allows lists of orbitals
• berry_phase now works for non-orthogonal basis sets (uses Lowdin transformation)
  This may require sufficiently small dk for accurateness.
• degenerate argument for conductivity to enable decoupling of states
• BandStructure.lineark now always starts from 0
• reading coordinates from siesta.out when bands are calculated #362
• complex warning for spin_moment #360 and #363
• partially fixed #102 (wavefunction for fxyz outside box, related to #365 and how origin is interpreted in the code
• non-collinear PDOS plotting
• improvement for BandStructure setup, arguments more stringent
• several fixes for sisl.viz; #368, #376 and #382
• empty array handlings in _sanitize_* #370
• ensured AtomicOrbital can be instantiated without specifying m (default to 0)
• fixed bug when copying orbitals
• fixed reading atomic labels in xsf files #402
• fixed hpc parameters #403

Changed

• order of arguments for nanoribbon it was not consistent with the others
• removed cell argument in Geometry.sub
• removed Sile.exist, refer to Sile.file which always will be a pathlib.Path instance
• berry_phase now uses the gauge=R convention, the code became much simpler
• BrillouinZone.parametrize function changed interface to allow more dimensions
• EigenStateElectron.inner does not use the overlap matrix by default, norm2 is for
  exactly this behaviour
• changed license to MPLv2 makes toolboxes easier to contribute under different license
• renamed origo to origin, see #365
• default parallel calculations are disabled
• changed State.align_* routines to align self rather than other
• doc fixes for recommending python -m pip

Removed

• removed keywords align for State.inner|outer, manually use align if required
• removed method State.expectation

toolbox.btd

Added

• calculation of scattering states and eigenchannels
• multiple variants of scattering state methods