Recent Releases of sisl

sisl - v0.16.2

A bugfix release for the wheels-generation (see 0.16.1 for details).

Full Changelog: https://github.com/zerothi/sisl/compare/v0.16.1...v0.16.2

- Python
Published by zerothi 9 months ago

Contributors

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

Isaac Alcon +
Nick Papior
Pol Febrer Calabozo

Pull requests merged

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

#913: updated to CODATA 2022
#914: Added support for I/O from zipfiles and buffers
#919: restructuring the read_scf for stdoutSileSiesta
#921: moved spinrotate and spinalign to physics/sparse

Maintenance pull requests merged

#915: Bump pypa/cibuildwheel from 2.23.2 to 2.23.3

Full Changelog: https://github.com/zerothi/sisl/compare/v0.16.0...v0.16.1

- Python
Published by zerothi 9 months ago

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 Calabozo
Thomas Frederiksen

What's Changed

Fixed matplotlib fatbands and enabled opacity by @pfebrer in https://github.com/zerothi/sisl/pull/862
Bump JamesIves/github-pages-deploy-action from 4.6.8 to 4.6.9 by @dependabot in https://github.com/zerothi/sisl/pull/866
Bump pypa/gh-action-pypi-publish from 1.11.0 to 1.12.2 by @dependabot in https://github.com/zerothi/sisl/pull/867
moved direct imports into a getattr segment by @zerothi in https://github.com/zerothi/sisl/pull/868
Cleanup of the plotables module by @pfebrer in https://github.com/zerothi/sisl/pull/870
allowed atoms in tbtnc, and enabled PDOS of ADOS in viz by @zerothi in https://github.com/zerothi/sisl/pull/871
Bump codecov/codecov-action from 4 to 5 by @dependabot in https://github.com/zerothi/sisl/pull/872
Bump pypa/cibuildwheel from 2.21.3 to 2.22.0 by @dependabot in https://github.com/zerothi/sisl/pull/876
streamlined projection options by @zerothi in https://github.com/zerothi/sisl/pull/875
Cython perf simplification by @zerothi in https://github.com/zerothi/sisl/pull/861
initial commit of nambu code by @zerothi in https://github.com/zerothi/sisl/pull/877
Bump JamesIves/github-pages-deploy-action from 4.6.9 to 4.7.1 by @dependabot in https://github.com/zerothi/sisl/pull/878
enabled ellipsis here and there by @zerothi in https://github.com/zerothi/sisl/pull/863
Bump JamesIves/github-pages-deploy-action from 4.7.1 to 4.7.2 by @dependabot in https://github.com/zerothi/sisl/pull/880
Bump pypa/gh-action-pypi-publish from 1.12.2 to 1.12.3 by @dependabot in https://github.com/zerothi/sisl/pull/881
enabled writing HSX files by @zerothi in https://github.com/zerothi/sisl/pull/884
Fixes for native hamiltonian format by @tfrederiksen in https://github.com/zerothi/sisl/pull/888
Test with nonorthogonal hamiltonian by @tfrederiksen in https://github.com/zerothi/sisl/pull/889
Bump pypa/gh-action-pypi-publish from 1.12.3 to 1.12.4 by @dependabot in https://github.com/zerothi/sisl/pull/890
Towncrier by @zerothi in https://github.com/zerothi/sisl/pull/893
Bump JamesIves/github-pages-deploy-action from 4.7.2 to 4.7.3 by @dependabot in https://github.com/zerothi/sisl/pull/895
Atom borders by @pfebrer in https://github.com/zerothi/sisl/pull/897
fixed and finalized BdG spin configuration by @zerothi in https://github.com/zerothi/sisl/pull/896
Bump pypa/cibuildwheel from 2.22.0 to 2.23.0 by @dependabot in https://github.com/zerothi/sisl/pull/899
enabled ufuncs for external classes by @zerothi in https://github.com/zerothi/sisl/pull/898
Bump pypa/cibuildwheel from 2.23.0 to 2.23.1 by @dependabot in https://github.com/zerothi/sisl/pull/903
Enabled fromsp with other than csr_matrix objects by @zerothi in https://github.com/zerothi/sisl/pull/904
Bump pypa/cibuildwheel from 2.23.1 to 2.23.2 by @dependabot in https://github.com/zerothi/sisl/pull/905
Fix fatbands plots when there is a jump in the band structure by @pfebrer in https://github.com/zerothi/sisl/pull/906
Git ignoring debug_info.py by @pfebrer in https://github.com/zerothi/sisl/pull/907
Formatting the argparse CLIs by @pfebrer in https://github.com/zerothi/sisl/pull/908

Full Changelog: https://github.com/zerothi/sisl/compare/v0.15.2...v0.16.0

- Python
Published by zerothi 11 months ago

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.

- Python
Published by zerothi about 1 year ago

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

- Python
Published by zerothi over 1 year ago

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 scaleatoms in favor of scalebasis 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.

- Python
Published by zerothi over 1 year ago

sisl - 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 infoattributes_ 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.

- Python
Published by zerothi over 2 years ago

sisl - 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)

- Python
Published by zerothi over 2 years ago

sisl - 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 SISLUNITSIESTA 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

- Python
Published by zerothi over 2 years ago

sisl - 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 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.

- Python
Published by zerothi about 3 years ago

sisl - 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)

- Python
Published by zerothi almost 4 years ago

sisl - 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
readfermilevel 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

- Python
Published by zerothi about 4 years ago

sisl - 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

- Python
Published by zerothi about 4 years ago

sisl - v0.11.0

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 spinorbitalmoment(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

Contributors

A total of 5 people contributed to this release.

Jonas Lundholm Bertelsen
Nick Papior
Pol Febrer
Sofia Sanz Wuhl
Thomas Frederiksen

Pull requests merged

A total of 12 pull requests were merged for this release.

#231 <https://github.com/zerothi/sisl/pull/231>__: Transmitting pbc to ASE
#246 <https://github.com/zerothi/sisl/pull/246>__: Method to calculate grid isosurfaces
#253 <https://github.com/zerothi/sisl/pull/253>_: Geometry.sanitize_atoms did not accept generic categories
#254 <https://github.com/zerothi/sisl/pull/254>__: f-string was not printing variable value due to missing f
#255 <https://github.com/zerothi/sisl/pull/255>__: Make parent categories callable and avoid their instantiation
#258 <https://github.com/zerothi/sisl/pull/258>__: Making coordinate categories more accessible
#263 <https://github.com/zerothi/sisl/pull/263>__: Supporting the creation of Binder docker images
#267 <https://github.com/zerothi/sisl/pull/267>__: bug: skewed isosurfaces were not properly calculated
#270 <https://github.com/zerothi/sisl/pull/270>__: Fixed reading geometries in .AXSF-files
#277 <https://github.com/zerothi/sisl/pull/277>__: maint: remove ending blank line when writing xyz-files
#298 <https://github.com/zerothi/sisl/pull/298>__: All plotly tests passing now
#300 <https://github.com/zerothi/sisl/pull/300>__: Make plotly docs work

- Python
Published by zerothi about 5 years ago

sisl - v0.10.0

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 (Thomas)
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

- Python
Published by zerothi over 5 years ago

sisl - v0.9.8

THIS WILL BE THE LAST Python2 release. All subsequent releases will be Python 3.6 and later (only!).

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.

- Python
Published by zerothi about 6 years ago

sisl - v0.9.7

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.

- Python
Published by zerothi over 6 years ago

sisl - v0.9.6

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

- Python
Published by zerothi over 6 years ago

sisl - v0.9.5

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

- Python
Published by zerothi over 7 years ago

sisl - v0.9.4

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

- Python
Published by zerothi over 7 years ago

sisl - v0.9.1

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.

- Python
Published by zerothi over 8 years ago

sisl - v0.9.0

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.

- Python
Published by zerothi over 8 years ago

sisl - v0.8.5

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.

- Python
Published by zerothi over 8 years ago

sisl - v0.8.4

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/writegeom => read/writegeometry read/writesc => read/writesupercell read/writees => read/writehamiltonian

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.

- Python
Published by zerothi over 8 years ago

sisl - v0.8.3

Fixed bug in _writedefault (should have been writedefault)
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 nosetests.

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.

- Python
Published by zerothi almost 9 years ago

sisl -

You are encouraged to update to this release which introduces many performance improvements and bug-fixes.

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 iterorbitals 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.

- Python
Published by zerothi almost 9 years ago

sisl - v0.8.1

You are heavily encouraged to update as this incorporates many new features and bug-fixes. - Fix a bug when reading non-Gamma TSHS files, now the supercell information is correct. - tbtncSileSiesta now distinguishes between: electronictemperature [K] and kT [eV] where the units are not the same. - Fixed TBTDN.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. - Shapes 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

- Python
Published by zerothi almost 9 years ago

sisl - v0.7.0

Initial release of sisl with proper DOI citation using Zenodo.

Changes: - Restructuring of the contained Sile's of the different linked DFT programs.

- Python
Published by zerothi about 9 years ago

sisl - v0.7.1

Enabled orthogonal Hamiltonian objects.

Implemented dH.nc file for TBtrans code.

- Python
Published by zerothi about 9 years ago

sisl - v0.7.5

Added Wannier90 support (reading of Wannier-Hamiltonian and Wannier-centres)

Enabled multiple Sile extensions with the same extension (by requesting specific classes).

Fixed things related to overlap matrices in the Hamiltonian structure. Added a few tests about the Hamiltonian.

- Python
Published by zerothi about 9 years ago

sisl - v0.7.6

API updates for Siles.

This release enhances the use of the implicit siles in sisl with a more stringent file name. - Added sdata script which parses the arguments based on the input file. This is preliminary work and will still change - Added XSF file format - Added bands file from siesta to easily plot band structures using python - Many bug-fixes for the IO of geometry read/write in rarely used file formats - Speeded up the Hamiltonian creation - Added code-coverage tests (mainly for developing reasons)

- Python
Published by zerothi about 9 years ago

sisl - v0.8.0

I am proud to announce the release of sisl 0.8.0.

Since this version one may easily install sisl using pypi or conda:

pypi install sisl conda install -c zerothi sisl

Release notes

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(dR, param) Hamiltonian.construct(func) or Hamiltonian.construct((dR, 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!

- Python
Published by zerothi about 9 years ago

Recent Releases of sisl

sisl - v0.16.2

sisl - v0.16.1

Contributors

Pull requests merged

Maintenance pull requests merged

sisl - v0.16.0

Contributors

What's Changed

sisl - v0.15.2

Contributors

Pull requests merged

Maintenance pull requests merged

Changelog

Added

Fixed

Changed

sisl - v0.15.1

Contributors

Pull requests merged

Added

Fixed

sisl - v0.15.0

Contributors

Pull requests merged

Added

Fixed

Removed

Changed

sisl - v0.14.3

Contributors

Pull requests merged

[0.14.3] - 2023-11-07

Added

Fixed

Changed

sisl - v0.14.2

Contributors

Pull requests merged

[0.14.2] - 2023-10-04

Fixed

Changed

sisl - v0.14.0

Contributors

Pull requests merged

[0.14.0] - 2023-09-28

Added

Changed

Fixed

toolbox.btd

Added

sisl - v0.13.0

Contributors

Pull requests merged

Added

Fixed

Changed

sisl - v0.12.2

Contributors

Pull requests merged

Added

Fixed

Changed

sisl - v0.12.1

Contributors

Pull requests merged

Added

Fixed

sisl - v0.12.0

Contributors

Pull requests merged

Added

Fixed

Changed

Removed

toolbox.btd

Added

sisl - v0.11.0

282

Contributors