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Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning once we hit release version 1.0.0.

[0.15.0] - YYYY-MM-DD

Added

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

  • 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

  • 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

  • removed Selector and TimeSelector, they were never used internally

Changed

  • 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

[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.

[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)

[0.14.1] - 2023-09-28

[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

[0.13.0] - 2023-1-18

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 80f27b05, 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.

[0.12.2] - 2022-5-2

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)

[0.12.1] - 2022-2-10

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

[0.12.0] - 2022-1-28

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/new.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

[0.11.0] - 2021-2-17

  • Major addition: plotly backend for plotting and interaction with output. This is still a work in progress made by Pol Febrer. Many thanks to @pfebrer!

  • Added unzip argument to BZ.apply methods to unzip multiple return values, also added documentation to reflect this

  • Fixed reading data-arrays from Siesta-PDOS files

  • Enabled minimization method for basis information and pseudo generation

  • Enabled plotting grids using the command-line

  • Bug in how non-colinear matrices are dealt with, now fixed Thanks to Xe Hu for discovering this.

  • Allowed reading the geometry for supercell HSX files Atomic coordinates and nsc are determined from xij arrays

  • Basic implementation of Hermitian construct. It now ensures a correct Hermitian matrix for simple cases

  • Added more return from close/within, supercell offsets may be queried (ret_isc)

  • Added more transposing functionality for spin matrices

  • Fixed wfsxSileSiesta returning proper k-points if a geometry is passed (i.e. reduced k-points). Otherwise warns users

  • Huge performance increase for finalizing very large structures

  • Fixed writing %block in fdf files

  • Enabled reading Fermi level from VASP DOSCAR files

  • Cleaned siesta and VASP reading of completed jobs, #287

  • added Geometry.new allowing easy type-lookups to convert to Geometry e.g. Geometry.new("RUN.fdf") and Geometry.new(ase_atoms) automatically figures out which method to call and how to interpret the objects. added Geometry.to allowing easy type-lookups to convert to other objects #282

  • enabled calculating supercell matrices with phases, format=sc: returns in supercell matrix form (no, no_s)

  • removed support for int and long as matrix types, only float/complex

  • Enabled sgrid to write tables of data

  • Merged spin_orbital_moment(deleted) and spin_moment with optional argument project

  • Enabled orbital resolved velocities

  • Added outSileSiesta.read_energy to read final energies in a property-dict (works both as a property (energy.fermi) and a dictionary (energy["fermi"])

  • Ensured ghost atoms in Siesta are handled with separate class, AtomGhost, #249

  • Using si.RealspaceSI with unfold=(1,1,1) no longer results in nsc on the given surface hamiltonian being set to (1,1,1).

  • Added calculation of isosurfaces, #246

  • Added sisl.WideBandSE for self-energies with constant diagonals

  • Enabled more user control over categories, #242

  • Improved interpolation function for Grid's, and also added filters

  • Bugfix for periodic directions for ASE conversion, #231

  • Fixed tuples for _sanitize_atoms, #233

  • Fixed reading correct unit from deltanc files, #234

  • Enabled berry-phase calculations for NC+SOC, #235

  • Added tiling to Grid, #238

  • Added Atoms.group_data which nicely splits an array holding orbital information into atomic contributions (a list since each sub-list may be unequal in length)

  • Many small bug-fixes and performance improvements

[0.10.0] - 2020-6-9

  • Exposing sisl_toolbox as a module for external contributions Now stuff contributed from 3rd parties can easily be included in a toolbox which is a separate module.

  • Changed asarray (as*) methods for SparseGeometry Now we have a dispatch class which enables one to store the behaviour as variables and then post-process

  • Using *.geom or geometry.atom is now deprecated, use *.geometry and geometry.atoms instead (respectively)

  • Added spin-rotation for density matrices, this will enable sisl to manipulate DM and write them for Siesta calculations

  • Enabled all numpy.ufuncs (np.exp(H))

  • Added nanoribbons construction (@tfrederiksen)

  • Internal change to pathlib for files and paths

  • Added velocity calculations for NC+SOC Hamiltonians

  • Sparse pattern transposes of non-full matrices, fixed bug

  • Changed Geometry.sort to be more diverse (this may break old code) This new way of sorting is way more flexible and allows very fine control, fixes #191, #197

  • Added a bilayer geometry which can create twisted bilayers #181, #186

  • Enabled VASP *CAR files to write/read dynamic specifications #185

  • Enabled xarray.DataArray returning from BrillouinZone objects #182

  • Several improvements to outSileSiesta.read_scf #174, #180

  • A huge performance increase for data extraction in tbtncSileTbtrans (thanks to Gaetano Calogero for finding the bottleneck)

  • Added preliminary usage of Mixers, primarily intented for extending sisl operations where SCF are used (may heavily change).

  • Lots of small bug-fixes

  • Now sisl is Python >=3.6 only, #162

This release was helped by the following committers (THANKS):

  • Thomas Frederiksen
  • Pol Febrer
  • Jonas Lundholm Bertelsen
  • Bernhard Kretz

[0.9.8] - 2020-2-10

  • fixed #160 by removing all(?) TRS k-points in a Monkhorst Pack grid

  • fixed repeat for SparseGeometryOrbital #161

  • changed lots of places for einsum in electron.py for increased performance

  • added AHC conductivity calculations conductivity (not tested)

  • added Berry curvature calculations berry_flux (not tested)

  • added Overlap class to directly use overlap matrices (without having a second matrix).

  • fixed geometry align issue when reading geometries from Siesta output #153

  • fixed pickling a sparse matrix #150

  • Fixed TSV.nc write-out for grid files (see poisson_explicit.py)

  • Fixed fermi level calculation for non-polarized calculations

  • Reverted Fermi calculation routine for more stable implementation

  • fixed DynamiclMatrix reading for number of atoms not divisable by 4 #145

A huge thanks to Jonas L. B. for fixes, suggestions etc.

[0.9.7] - 2019-9-26

  • Bug-fix for reading geometries in outSiesta

  • Enabled reading the fermi level from the output, fixes #126

  • Enabled Siesta STM and STS output

  • Fixed an inheritance issue in axsfSile which meant it was unusable until now

  • Maintenance fix for looping sparse matrices. Now the default is to loop the sparse non-zero elements. If one wishes to loop all atoms/orbitals one should use iter_orbitals() NOTE: This may break some codes if they used loops on sparse matrices

  • Fixed reading VASP CAR files with constraints (thanks to T. Frederiksen)

  • Added overlap method to Geometry to find overlapping atoms between two geometries.

  • Added Siesta LDOS charge handling

  • Changed edges method to not exclude it-self by default. This is because it is not intuitive given the default exclude=None

    Note: this may break compatibility with other software/scripts.

  • Added mulliken charge calculations and orbital angular momentum for SO DM, fixes #136

  • Fixed reading overlap matrix in conjunction with DM from fdf-sile

  • Performance increase for the real-space self-energy calculations

  • Fixed transposing of the spin-box for NC and SO matrices

  • Enabled TRS handler for SO matrices, fixes #125

  • Enabled better b-casting assignments for sparse-matrices, fixes #134

  • Upgraded documentation to a layout that obeys numpydoc

  • Fixed reading ASE xyz outputs, thanksto JL. Bertelsen,

  • Fixed a typo in fdf reading onlyS, thanks to JL. Bertelsen, #135

  • Enabled reading arbitrary self-energy by requesting an energy and k-point from TSGF files.

  • Upgraded handling of TBT.*.nc files to conform with the >=Siesta-4.1-b5 releases where all files contain the same device + electrode meta-data.

  • Deprecated TBTGFSileTBtrans (use tbtgfSileTBtrans instead)

  • Forced align=False in inner such that users should take care of this

  • Added align_norm to swap states such that they more or less correspond to the same band (which should have a closer residual for on-site coefficients).

  • Removed norm2 and made norm equal to norm2 for states. This is the more natural thing, besides. Doing norm() ** 0.5 shouldn't be too much of a problem.

[0.9.6] - 2019-6-18

  • Officially added real-space self-energy calculations

  • Cleaned TBT vs. PHT for class name structures

  • Bugfix for reading MD output from Siesta out-files #130

  • Bugfix for tbtse files when requesting pivoting indices using this combination in_device=True, sort=False which in most cases return wrong indices, thanks to J. Bertelsen for bug-find!

  • Added several routines for retrieving transposed coupling elements. When having connections i -> j it may be beneficial to easily get the transposed connection j -> i by taking into account the supercell. Geometry.a2transpose enables this functionality making construct functions much simpler when having edges/boundaries.

  • Bug-fix for reading white-space prefixed keywords in XSF files, #127

  • Performance increase for self-energy calculations for very small systems

  • Huge memory reduction for Geometry.o2a with very large system

  • Enabled pickling on BrillouinZone objects

  • Added spin_moment to Hamiltonian

  • Removed rotate[abc] methods since they were cluttering the name-space Codes should simply replace with:

    geometry.rotate(angle, geometry.cell[{012}, :], *)

    for the same effect.

  • Finally removed deprecated write_geom from the API

  • Enabled calculation of <S^2> for spin-polarized calculations, this may be used for calculating spin-contaminations

  • added checks for SparseCSR to disallow out-of-bounds keys

  • Bug fixed for reading POSCAR files from VASP (only when multiple species are used in a non-ordered fashion)

  • added sisl command line utility, it is exactly the same as sdata

  • Enabled pickling sparse matrices, this allows dask usage of sparse matrices

  • Performance increase for sparse matrix handling

  • Fixed a problem with Fortran IO + Jupyter notebooks, now the file-handles are re-used if a code block is terminated before closing the file

  • Added SparseOrbital append + transpose This enables appending Hamiltonian's (append) and makes hermiticity checks possible (transpose)

  • Enabled complex averaged calculations using oplist The oplist object is a container allowing inter-element operations

    >>> l1 = oplist([0, 1])
>>> l2 = oplist([2, 3])
>>> l = l1 + l2
>>> print(l)
[2, 4]

    This is extremely handy for BrillouinZone.asaverage/assum when calculating multiple values using eigenstate objects.

  • Added reflection calculation to tbtncSileTBtrans

  • Added more distribution functions (step and heaviside)

  • Removed numpy deprecated class numpy.matrix, now everything is array

  • Removed possibility of using kavg=list(...) due to complexity, now single kavg requests are not k-averaged.

  • Bugfix in calculating shot_noise, noise_power and fano factors in tbtncSileSiesta They were only correct for Gamma-point calculations

  • Fixed *.EIG sdata processing when using --dos

  • Fixed reading geometries from grids from VASP (grid values were correct)

  • Toolboxes:

    • Added a toolbox to calculate the Poisson solution for arbitrary electrodes for TranSiesta

[0.9.5] - 2018-11-12

  • Fixed temperature for phonon output pht*nc files

  • Added tbtprojncSileTBtrans sile for analyzing projected transmissions

  • Removed deprecated dhSileTBtrans

  • Bug fix for binary grid files with Siesta and also reads using fdf-files

  • Changed default self-energy eta values to 1e-4 eV

  • Added Zak-phase calculations (thanks to T. Frederiksen)

  • Updated lots of State methods

  • added Bloch expansion class which can expand any method

  • self-energy calculations:

    • Much faster
    • enabled left/right self-energies in one method

  • fixed AtomicOrbital copies

  • enabled TSGF reads

  • Added noise-power calculations for TBT.nc files

  • Fixed TBT.SE.nc files, units and scattering matrix retrieval

  • added more VASP files

[0.9.4] - 2018-8-4

  • Fixes for the GULP dynamical matrix reads

  • Enabled preliminary reads of OpenMX input file

  • Enabled DOS calculation for the eigenvalue files

  • Added Berry-phase calculation for orthogonal basis sets

  • Added velocity calculation of electronic eigenstates

  • Enabled effective mass tensor in electronic eigenstates (un-tested)

  • High performance increase by moving stuff to Cython.

  • Added Siesta interaction tutorials

  • Added orthogonality checks when reading sparse matrices

  • Lots of fixes for the fdf-file

  • Added Mulliken calculation in DensityMatrix/EnergyDensityMatrix

  • Enabled reading phonons from FC files

  • Added named-groups which enables accessing groups of atoms by names.

    Geometry['Hello'] = [2, 3, 4]

  • Changed Hessian to DynamicalMatrix to clarify the units

  • Added new units class to handle complex units.

  • Enabled a Phonon class to calculate group velocities of phonons, DOS and PDOS, displacements

  • Bug-fixes for Siesta binary writes, now the supercell format is always Siesta compliant.

  • Enabled replacing k-points in MonkhorstPack grids.

  • Enabled calculation of band-velocities from eigenstates

  • Made better progress-bars. Using eta= now relies on tqdm It is however still an optional dependency.

  • Fixed Gamma-point periodic wavefunction storage. Creating grids with wave-functions is fully functional for arbitrarily big supercells.

  • BrillouinZone objects:

    • Renamed PathBZ to BandStructure

    • Renamed MonkhorstPackBZ to MonkhorstPack

    • Enabled MonkhorstPack symmetry. This will reduce the number of k-points to roughly half (note symmetry is by default on)

    • Forced MonkhorstPack to create a k-grid which is Gamma centered

  • Shapes (backwards compatibility broken)

    • Complete re-write of Shapes

    • Skewed Cuboids, Ellipsoids

    • Set combinations of Shapes (unions, difference sets, etc.)

  • Grid

    • Enabled Grid.index for shapes.

    • Fixed grid initialization to create grid spacings fixed by a real. I.e. the voxel spacing.

      >>> Grid([10, 10, 10]) # 10 points per lattice vector
>>> Grid(0.1) # 0.1 Angstrom spacing

    • Enabled plotting wavefunctions on grids.

    • Enabled plotting charge density on grids.

  • Enabled tqdm usage for progressbar. It is fast and easy to use and a small requirement. (still optional)

  • Added intrinsic Sisl exceptions which will be used throughout (at some point)

  • Removed deprecated TightBinding class (use Hamiltonian instead)

  • Added many SislWarning raises which are used to notify the user of potentially important things (say if sisl knows there should be a unit associated but it couldn't find it).

  • Added TSDE file reading in sisl.

  • Siesta reading of grid-related data is now much smarter. It will try and recognize the units of the data so the units become sisl intrinsics (Ry -> eV, Bohr -> Ang, etc.). This means that typically one does not need to do manual unit-conversion. There are however a few cases where sisl cannot figure out the units. Particularly if the files are renamed.

  • Added a new class EigenSystem which holds information regarding eigenvalues and eigenvectors.

    • Currently an EigenState class is also enabled which can currently be used to calculate wavefunctions, DOS, PDOS and more to come.

  • Fixed lots of bugs in fdf-reading quantities. Now one is also able to read Hamiltonian and other physical quantities from the fdf-object directly. There is pre-defined orders of which files to read from if there are multiple files eligeble.

    Reading the geometry now defaults to the fdf file, but one can query the output files by a boolean.

  • Enabled PDOS calculations for the Hamiltonian. Together with the MonkhorstPack class one can easily calculate k-averaged PDOS quantities.

  • Fixed cube reading/writing of multi-column data.

  • Added siesta PDOS xml parsing, currently this is only scriptable but it manages easy extraction of quantities without the PDOSXML utility. This also enables retrieving the PDOS as an xarray.DataArray.

  • Fixed a bug in writing XV files (only for -100/-200 species)

  • TBtrans / TBT.nc file:

    • Added TBT.SE.nc file to enable easy extraction of self-energies from TBtrans

    • Added COOP and COHP extraction to the TBT.nc files.

    • Added DM and ADM extraction to the TBT.nc files.

    • Reorganized the TBtrans netcdf files (internal changes only)

    • Added shot-noise calculation (and Fano factor). Currently un-tested!

  • Several added files

[0.9.3] - 2018-8-4

[0.9.2] - 2017-10-25

  • Various minor bug-fixes

[0.9.1] - 2017-10-23

  • Fixed scaling of bond-currents in case 'all' is used, makes comparison with '+' and '-' easier.

  • Updated defaults in bond_current to '+' such that only forward going electrons are captured.

  • Updated defaults in vector_current to '+' such that only forward going electrons are captured.

[0.9.0] - 2017-10-16

  • Enabled reading a tabular data-file

  • Lots of updates to the spin-class. It should now be more coherent.

  • Added rij and Rij to the sparse_geometry classes to extract orbital or atomic distance matrices (returing the same sparsity pattern).

  • Renamed which keyword in Geometry.center to what

  • Added uniq keyword to o2a for better handling of orbitals -> atoms.

  • Fixed a performance bottleneck issue related to the scipy.linalg.solve routine which was changed since 0.19.0.

  • Changed internal testing scheme to pytest

  • Lots of bug-fixes here and there

  • Geometry files used in the command-line has updated these arguments:

    • tile
    • repeat
    • rotate

    The order of the arguments are interchanged to be similar to the scripting capabilities.

    Also fixed an issue related to moving atoms into the unit-cell.

  • Enabled deleting supercell elements of a sparse Geometry. This will come in handy when calculating the self-energies and Green functions. I.e. Hamiltonian.set_nsc(...) will truncate entries based on the new supercell.

  • Preliminary testing of reading Siesta binary output (.RHO, .VT, etc.)

  • Added parsing the Siesta EIG file (easy plotting, reading in Python)

  • Changed interface for BrillouinZone objects. Now a BrillouinZone accepts any object which has cell/rcell entries. Any function call on the BrillouinZone object will transfer the call to the passed object and evaluate that function for all k-points in the BrillouinZone.

  • sisl.io.siesta.tbtrans

    • Added current calculator to TBT.nc sile to calculate the current as TBtrans does it (this requires the latest commit in SIESTA which defines the chemical potential and electronic structure of all electrodes).

    • Bug-fixes for TBT.nc sile, the bond-currents for multi-orbital systems were in some cases wrong.

    • Huge performance increase for TBT.nc data processing. Now the majority of routines are based on array-indexing, rather than sparse loops.

    • Changed the DOS retrieval functions to be more flexible. The default is now to return the summed DOS across the selected atoms.

    • Added a TBTGFSileSiesta which enables one to create external self-energies to be read in by TBtrans (complete electrode control).

    • Added deltancSileSiesta as a replacement for dHncSileSiesta, TBtrans 4.1b4 will have two delta terms, dH (adds to bond-currents) and dSigma (does not add to bond-currents).

    • BEWARE, lots of defaults has changed in this release.

  • Hamiltonian.tile is now even faster, only utilizing intrinsic numpy array functionality.

  • Greatly speeded up Hamiltonian.remove/sub functions. Now there are no for-loops in the remove/sub routines which will greatly increase performance. It will now be much faster to generate the Hamiltonian for a small reference cell, tile/repeat it, remove atoms.

[0.8.5] - 2017-7-21

  • Added the following routines:

    • SuperCell.fit routine to determine a new supercell object such that a given set of coordinates are all within AND periodic in the new supercell.
    • SuperCell.parallel to check whether two objects have parallel latticevectors.
    • Geometry.distance returns a list of distances from a given set of atoms. I.e. to determine a set of distances required for a subsequent close call. This routine can also be used to group neighbouring atoms in a common fashion.
    • Geometry.optimize_nsc loops all atoms and minimizes nsc in case one is not sure of the interaction range.
    • Hamiltonian.shift enables the shift of the entire electronic structure Fermi-level.
    • Added new flag to Hamiltonian.Hk routines format={'csr', 'array', 'dense', ...} to ensure a consistent return of the data-type.

  • Bug fix for dHncSileSiesta for multiple levels.

  • Performance boost for the sub and remove functions for the Hamiltonian objects. Instead of creating the geometry first, it may now be much faster to generate the small Hamiltonian, tile -> repeat -> sub -> remove.

  • Performance boost for the tile and repeat functions for the Hamiltonian objects. They are now the preferred method for creating large systems.

  • Bug fixed when having extremely long atomic ranges and using tile/repeat. The number of supercells was too large. It did not affect anything, but it was inconsistent.

  • Enabled reading the density matrix and energy density matrix from siesta.

  • Addition of a PerformanceSelector class which enables a dynamic selection of the best routine.

    Currently this is enabled in the SparseOrbitalBZ class where constructing a matrix @ k can be done in numerous ways.

  • Bug fixed in supercell specification of the Hamiltonian:

    >>> H[io, jo, (-1, 0, 0)]

    now works in all cases.

  • Spin-orbit H(k) has been enabled

  • Fixed reading the <>.nc file from SIESTA, the non-zero elements count was wrong.

  • Now H(k) has been tested for non-colinear and spin-orbit coupling and one can now use sisl to perform non-colinear and spin-orbit coupling calculations.

  • API change, all dR keywords has been changed to R for consistency and reduction of ambiguity. Also the Atoms.dR is now referred to as Atoms.maxR() to indicate its meaning.

    This may break old scripts if one use the dR keyword in arguments.

[0.8.4] - 2017-6-11

  • Added BrillouinZone class to easily create BrillouinZone plots etc. When calculating the eigenspectrum of a Hamiltonian one may pass the BrillouinZone object instead of the k-point to retrieve all eigenvalues for the k-points in the BrillouinZone object. Say for a PathBZ one can now easily retrieve the band-structure.

  • Enabled specification of Hamiltonian connections across supercells via a tuple index (as the last index):

    >>> H[io, jo, (-1, 0, 0)]

    Thus connecting orbital io and jo across the -1 first lattice vector

  • Enabled tbtrans files to attach a geometry (to get correct species).

  • API change of:

    read/write_geom => read/write_geometry
read/write_sc => read/write_supercell
read/write_es => read/write_hamiltonian

    Moved quantity to physics.

  • Enabled slice deletion in SparseCSR

    Enabled eliminate_zeros() to remove unneeded values.

  • Added ScaleUp compatibility. sisl now acceps ScaleUp files which is a 2nd principles code for large scale calculations using Wannier functions.

  • Added Hamiltonian.sub/remove/tile for easy extension of Hamiltonian without having to construct the larger geometries. This should speed up the creation of really large structures as one may then simply "update" the Hamiltonian elements subsequently.

[0.8.3] - 2017-4-5

  • Fixed bug in __write_default (should have been _write_default)

  • API change in close functions, now ret_coord => ret_xyz, ret_dist => ret_rij

  • Added SparseCSR math operations work on other SparseCSR matrices Thus one may now do:

    >>> a, b = SparseCSR(...), SparseCSR(...)
>>> aMb, aPb = a * b, a + b

    Which makes many things much easier. If this is used, you are encouraged to assert that the math is correct. Currently are the routines largely untested. Assistance is greatly appreciated in creating tests.

  • Geometries now always create a supercell. This was not the case when an atom with no defined orbital radius was used. Now this returns a supercell with 10 A of vacuum along each Cartesian direction.

[0.8.2] - 2017-3-31

  • Fixed reading _hr.dat from Wannier90, now the band-structure of SrTiO3 (Junquera's test example) is correct.

  • Speeded up tbtrans.py analyzing methods enourmously by introducing faster sparse iterators. Now one can easily perform data-analysis on systems in excess of 10.000 atoms very fast.

  • Added the TBT.AV.nc file which is meant to be created by sisl from the TBT.nc files (i.e. create the k-averaged output). This enables users to run tbtrans, create the k-averaged output, and then delete the old file to heavily reduce disk-usage.

    An example:

    tbtrans RUN.fdf > TBT.out
sdata siesta.TBT.nc --tbt-av
rm siesta.TBT.nc

    after this siesta.TBT.AV.nc exists will all k-averaged quantites. If one is not interested in k-resolved quantities this may be very interesting.

  • Updated the TBT.nc sile for improved readability.

  • Easier script data-extraction from TBT.nc files due to easier conversion between atomic indices and pivoting orbitals.

    For this:

    • a2p returns the pivoting indices for the given atoms (complete set)

    • o2p returns the pivoting indices for the given orbitals

    • Added atom keyword for retrieving DOS for a given set of atoms

    • sdata and TBT.nc files now enable the creation of the TBT.AV.nc file which is the k-averaged file of TBT.nc

  • Faster bond-current algorithms (faster iterator)

  • Initial template for TBT.Proj files for sdata processing

  • Geometry:

    • Enabled multiplying geometries with integers to emulate repeat or tile functions:

      >>> geometry * 2 == geometry.tile(2, 0).tile(2, 1).tile(2, 2)
>>> geometry * [2, 1, 2] == geometry.tile(2, 0).tile(2, 2)
>>> geometry * [2, 2] == geometry.tile(2, 2)
>>> geometry * ([2, 1, 2], 'repeat') == geometry.repeat(2, 0).repeat(2, 2)
>>> geometry * ([2, 1, 2], 'r') == geometry.repeat(2, 0).repeat(2, 2)
>>> geometry * ([2, 0], 'r') == geometry.repeat(2, 0)
>>> geometry * ([2, 2], 'r') == geometry.repeat(2, 2)

      This may be considered an advanced feature but useful nonetheless.

    • Enabled "adding" geometries in a similar way as multiplication I.e. the following applies:

      >>> A + B == A.add(B)
>>> A + (B, 1) == A.append(B, 1)
>>> A + (B, 2) == A.append(B, 2)
>>> (A, 1) + B == A.prepend(B, 1)

    • Added origo and atom argument to rotation functions. Previously this could be accomblished by:

      rotated = geometry.move(-origo).rotate(...).move(origo)

      while now it is:

      rotated = geometry.rotate(..., origo=origo)

      The origo argument may also be a single integer in which case the rotation is around atom origo.

      Lastly the atom argument enables only rotating a sub-set of atoms.

    • Geometry[..] is now calling axyz if .. is pure indices, if it is a slice it does not work with super-cell indices

    • Added rij functions to the Geometry for retrieving distances between two atoms (orij for orbitals)

    • Renamed iter_linear to iter

    • Added argument to iter_species for only looping certain atomic indices

    • Added iter_orbitals which returns an iterator with atomic and associated orbitals. The orbitals are with respect to the local orbital indices on the given atom

      >>> for ia, io in Geometry.iter_orbitals():
>>>     Geometry.atom[ia].R[io]

      works, while

      >>> for ia, io in Geometry.iter_orbitals(local=False):
>>>     Geometry.atom[ia].R[io]

      does not work because io is globally defined.

    • Changed argument name for coords, atom instead of the old idx.

    • Renamed function axyzsc to axyz

  • SparseCSR:

    • Added iter_nnz(i=None) which loops on sparse elements connecting to row i (or default to loop on all rows and columns).

    • ispmatrix to iterate through a scipy.sparse.*_matrix (and the SparseCSR matrix).

  • Hamiltonian:

    • Added iter_nnz which is the Hamiltonian equivalent of SparseCSR.iter_nnz. It enables explicit looping on atomic couplings, or orbital couplings. I.e. one may specify a subset of atoms or orbitals to loop over.

    • Preliminary implementation of the non-collinear spin-case. Needs testing.

[0.8.1] - 2017-2-23

  • Fix a bug when reading non-Gamma TSHS files, now the supercell information is correct.

  • tbtncSileSiesta now distinguishes between: electronic_temperature [K] and kT [eV] where the units are not the same.

  • Fixed TBT_DN.nc TBT_UP.nc detection as a Sile

  • Added information printout for the TBT.nc files

     sdata siesta.TBT.nc --info

    will print out what information is contained in the file.

  • Atoms overhauled with a lot of the utility routines inherent to the Geometry object. It is now much faster to perform operations on this object.

  • The FDF sile now allows setting and retrieving variables from the fdf file. Hence one may now set specific fdf flags via:

     sdata RUN.fdf --set SolutionMethod Transiesta

  • Changed default output precision for TXT files to .8f. Additionally one may use flag --format in sgeom to define the precision.

  • Shape have been added. There are now several Shapes which may be used to easily find atoms within a given Shape. This should in principle allow construction of very complex Shapes and easier construction of complex Hamiltonians

[0.8.0] - 2017-1-7

This release introduces many API changes and a much more stream-lined interface for interacting with sisl.

You are heavily encouraged to update your distribution.

Here is a compressed list of changes:

  • sdata is now an input AND output dependent command. It first reads the input and output files, in a first run, then it determines the options for the given set of files. Secondly, the sdata command uses "position dependent" options. This means that changing the order of options may change the output.

  • tbtncSile

    • Correct vector currents (for xsf files)
    • bug-fix for Gamma-only calculations
    • returned DOS is now correctly in 1/eV (older versions returned 1/Ry)
    • fixed sdata atomic[orbital] ranges such that, e.g. --atom [1-2][3-5] (for atom 1 and 2 and only orbitals 3, 4 and 5 on those atoms.)
    • DOS queries now has an extra argument (E) which returns only for the given energy.
    • When storing tables in sdata this now adds information regarding each column at the top (instead of at the bottom). Furthermore, the information is more descriptive

  • Changed all square named arguments to orthogonal

  • Added nsc field to xyz files (to retain number of supercells)

  • Added move function for geometry (same as translate)

  • Added prepend function, equivalent to append, but adding the atoms in the beginning instead of the end

  • Fixed many bugs related to the use of Python-ranges (as opposed to numpy ranges)

  • SparseCSR now enables operations:

    a = SparseCSR(...)
a = a * 2 + 2

    is now viable. This enables easy scaling, translation etc. using the sparse matrix format (very handy for magnetic fields).

  • Enabled del for SparseCSR, i.e. del SparseCSR(..)[0, 1] will remove the element, completely.

  • Enabled reading of the TSHS file from SIESTA 4.1, now we may easily interact with SIESTA.

  • Moved version.py to info.py

  • Moved scripts to entry_points, this makes scripts intrinsic in the module and one may import and use the commands as their command-line equivalents.

  • Hamiltonian.construct now takes a single argument which is the function for the inner loop. The old behaviour may be achieved by doing either:

    >>> func = Hamiltonian.create_construct(R, param)
>>> Hamiltonian.construct(func)

    or

    >>> Hamiltonian.construct((R, param))

  • The atoms contained in the Geometry are now not duplicated in case of many similar Atom objects. This should reduce overhead and increase throughput. However, the efficiency is not optimal yet.

  • Added many more tests, thus further stabilizing sisl

    I would really like help with creating more tests! Please help if you can!