sisl

Electronic structure Python package for post analysis and large scale tight-binding DFT/NEGF calculations

Science Score: 67.0%

This score indicates how likely this project is to be science-related based on various indicators:

✓
CITATION.cff file
Found CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
✓
.zenodo.json file
Found .zenodo.json file
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DOI references
Found 8 DOI reference(s) in README
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Academic publication links
Links to: zenodo.org
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Committers with academic emails
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Institutional organization owner
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (19.5%) to scientific vocabulary

Keywords

bigdft condensed-matter density-functional-theory dft geometry graphene gulp negf physics siesta solid-state solid-state-physics tbtrans tight-binding transiesta vasp wannier90

Keywords from Contributors

interactive periodic-table mesh interpretability computational-chemistry sequences quantum-chemistry generic projection standardization

Last synced: 6 months ago · JSON representation ·

Repository

Electronic structure Python package for post analysis and large scale tight-binding DFT/NEGF calculations

Basic Info

Host: GitHub
Owner: zerothi
License: mpl-2.0
Language: Python
Default Branch: main
Homepage: https://zerothi.github.io/sisl
Size: 552 MB

Statistics

Stars: 212
Watchers: 16
Forks: 62
Open Issues: 102
Releases: 32

Topics

bigdft condensed-matter density-functional-theory dft geometry graphene gulp negf physics siesta solid-state solid-state-physics tbtrans tight-binding transiesta vasp wannier90

Created over 10 years ago · Last pushed 6 months ago

Metadata Files

Readme Changelog Contributing Funding License Code of conduct Citation

sisl

sisl is an open-source easy-to-use density functional theory API framework to post-analyse density functional theory codes output as well as providing tight-binding calculation capabilities. It couples to a wide range of density functional theory codes and has a high connection with LCAO codes such as Siesta. The tight-binding matrices can be used in non-equilibrium Green function calculations with TBtrans as a backend. API for creating publication ready graphs and images.

Features

Simple command-line interface: To extract or quickly plot calculation output
Tight-binding API: Easily create (non-) orthogonal tight-binding matrices and do electronic structure analysis
Manipulation of sparse matrices: Extract, replace, append matrices and sub-matrices to one another
Post analyse DFT simulations: Post-process LCAO Hamiltonians by doing (projected) density of states, inverse participation ratio and many more
Post analyse NEGF simulations: Effectively create and post-analyse NEGF output from TBtrans
Real-space grid analysis: Perform mathematical operations on DFT real-space grid outputs, spin-density differences and wavefunction plots
Conversion of geometries and real-space grid: Easy conversion of geometry files and real-space grid file formats (cube, xsf, etc.)
User contributed toolboxes: Users may contribute toolboxes for sharing methodologies
Interoperability with other codes: ASE and pymatgen
and many more features

Tutorials and examples

The easiest way to get started is to follow the tutorials here and the workshop material for TranSiesta here.

Documentation

Please find documentation here:

Community support

There are different places for getting information on using sisl, here is a short list of places to search/ask for answers:

Ask questions on the Discord page
Ask questions on the Github issue page
Documentation, recommended reference page
Workshop examples showing different uses

If sisl was used to produce scientific contributions, please use this DOI for citation. We recommend to specify the version of sisl in combination of this citation:

@software{zerothi_sisl,
  author = {Papior, Nick},
  title  = {sisl: v<fill-version>},
  year   = {2025},
  doi    = {10.5281/zenodo.597181},
  url    = {https://doi.org/10.5281/zenodo.597181}
}

To get the BibTeX entry easily you may issue the following command:

sdata --cite

which fills in the version number.

Contributing

Kindly read our Contributing Guide to learn and understand about our development process, how to propose bug fixes and improvements, and how to build and test your changes to sisl.

Contributors

License

Owner

Name: Nick Papior
Login: zerothi
Kind: user
Location: Kgs. Lyngby, Denmark
Company: @dtudk

Repositories: 40
Profile: https://github.com/zerothi

Citation (CITATION.cff)

version: 0.16.2
commit: "v0.16.2"
date-released: "2025-04-10"
cff-version: 1.2.0
message: "Please cite sisl in any paper to acknowledge and support development."
type: software
authors:
  - family-names: Papior
    given-names: Nick
    orcid: "https://orcid.org/0000-0003-3038-1855"
    alias: zerothi
  - family-names: Febrer Calabozo
    given-names: Pol
    orcid: "https://orcid.org/0000-0003-0904-2234"
    alias: pfebrer
title: sisl
identifiers:
  - description: "Collection DOI for any sisl version."
    type: doi
    value: 10.5281/zenodo.597181
url: https://github.com/zerothi/sisl
repository-code: https://github.com/zerothi/sisl
license: MPL-2.0
keywords:
  - physics
  - tight-binding
  - DFT
  - LCAO
  - NEGF

GitHub Events

Total

Create event: 40
Commit comment event: 4
Release event: 2
Issues event: 68
Watch event: 26
Delete event: 38
Issue comment event: 235
Push event: 225
Pull request review comment event: 134
Pull request review event: 81
Pull request event: 92
Fork event: 4

Last Year

Create event: 40
Commit comment event: 4
Release event: 2
Issues event: 68
Watch event: 26
Delete event: 38
Issue comment event: 235
Push event: 225
Pull request review comment event: 134
Pull request review event: 81
Pull request event: 92
Fork event: 4

Committers

Last synced: about 2 years ago

All Time

Total Commits: 4,188
Total Committers: 9
Avg Commits per committer: 465.333
Development Distribution Score (DDS): 0.085

Past Year

Commits: 456
Committers: 5
Avg Commits per committer: 91.2
Development Distribution Score (DDS): 0.162

Top Committers

Name	Email	Commits
Nick Papior	n**r@g**m	3,834
Pol Febrer	p**6@g**m	195
Thomas Frederiksen	t**n@e**s	94
Jonas Lundholm Bertelsen	d**b@g**m	42
dependabot[bot]	4****]	11
Nils Wittemeier	n**r@g**m	5
A.H. Kole	a**e@u**l	3
Sofia Sanz Wuhl	s**2@g**m	3
lgtm-com[bot]	4****]	1

Committer Domains (Top 20 + Academic)

uu.nl: 1 ehu.eus: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 225
Total pull requests: 353
Average time to close issues: 7 months
Average time to close pull requests: about 1 month
Total issue authors: 31
Total pull request authors: 10
Average comments per issue: 4.48
Average comments per pull request: 5.48
Merged pull requests: 306
Bot issues: 0
Bot pull requests: 59

Past Year

Issues: 40
Pull requests: 90
Average time to close issues: 23 days
Average time to close pull requests: 1 day
Issue authors: 10
Pull request authors: 5
Average comments per issue: 3.3
Average comments per pull request: 2.64
Merged pull requests: 78
Bot issues: 0
Bot pull requests: 30

View more stats

Top Authors

Issue Authors

zerothi (115)
pfebrer (26)
tfrederiksen (21)
AsymmetryChou (8)
AleksBL (6)
masume70 (4)
rreho (4)
ahkole (4)
juijan (4)
apezol (3)
novidad21 (3)
oroszl (2)
nils-wittemeier (2)
JoshRackers (2)
danielpozsar (2)

Pull Request Authors

pfebrer (130)
zerothi (121)
dependabot[bot] (73)
tfrederiksen (50)
nils-wittemeier (8)
juijan (3)
arsalan-akhtar (2)
ahkole (1)
lgtm-com[bot] (1)
ialcon (1)

Top Labels

Issue Labels

feature (8) enhancement (5) question (2) todo (1) doc (1) discussion (1) low-priority (1) help wanted (1) bug (1) high-priority (1)

Pull Request Labels

dependencies (73) github_actions (32) python (3)

Packages

Total packages: 2
Total downloads:
- pypi 2,560 last-month
Total docker downloads: 13

Total dependent packages: 5
(may contain duplicates)
Total dependent repositories: 7
(may contain duplicates)
Total versions: 60
Total maintainers: 1

pypi.org: sisl

Manipulation and post-processing of DFT output and creating tight-binding models for NEGF transport

Homepage: https://zerothi.github.io/sisl
Documentation: https://zerothi.github.io/sisl
License: MPL-2.0
Latest release: 0.16.2
published 9 months ago

Versions: 49
Dependent Packages: 4
Dependent Repositories: 6
Downloads: 2,560 Last month
Docker Downloads: 13

Rankings

Dependent packages count: 3.2%

Docker downloads count: 4.1%

Average: 5.5%

Forks count: 5.6%

Stargazers count: 5.7%

Dependent repos count: 6.0%

Downloads: 8.4%

Maintainers (1)

zeroth

Last synced: 6 months ago

conda-forge.org: sisl

sisl is a tool to manipulate density functional theory code input and/or output. It also implements tight-binding tools to create and manipulate multi-orbital (non)-orthogonal basis sets.

Homepage: https://github.com/zerothi/sisl
License: MPL-2.0
Latest release: 0.12.2
published almost 4 years ago

Versions: 11
Dependent Packages: 1
Dependent Repositories: 1

Rankings

Dependent repos count: 24.4%

Forks count: 25.3%

Average: 27.2%

Dependent packages count: 29.0%

Stargazers count: 30.2%

Last synced: 6 months ago

Dependencies

pyproject.toml pypi

netCDF4 *
numpy >=1.21.5 ; sys_platform == 'win32' and python_version >= '3.10'
numpy >=1.19.5 ; sys_platform == 'win32' and python_version <= '3.9'
numpy >=1.13 ; sys_platform != 'win32'
pyparsing >=1.5.7
scipy >=1.5.0

docs/requirements.txt pypi

cython *
dill >=0.3.2
ipykernel *
ipywidgets ==7.7.1
jupyterlab-widgets ==1.1.1
kaleido *
matplotlib *
nbsphinx *
netCDF4 *
numpy >=1.13
pathos *
plotly *
pyparsing >=1.5.7
scikit-image *
scipy >=1.5.0
setuptools >=46.0
setuptools_scm >=6.2
sphinx-gallery *
sphinx-rtd-theme *
tqdm *
wheel *
xarray >=0.10.0

requirements.txt pypi

netCDF4 *
numpy >=1.13
pyparsing >=1.5.7
scipy >=1.5.0

.github/workflows/codeql.yml actions

actions/checkout v3 composite
github/codeql-action/analyze v2 composite
github/codeql-action/autobuild v2 composite
github/codeql-action/init v2 composite

.github/workflows/documentation_ghpages.yaml actions

JamesIves/github-pages-deploy-action 4.4.1 composite
actions/checkout v3 composite
actions/setup-python v4 composite
r-lib/actions/setup-pandoc v2 composite

.github/workflows/test.yaml actions

actions/checkout v3 composite
actions/setup-python v4 composite
codecov/codecov-action v2 composite

.github/workflows/wheels.yaml actions

actions/checkout v3 composite
actions/download-artifact v3 composite
actions/setup-python v4 composite
actions/upload-artifact v3 composite
awvwgk/setup-fortran main composite
pypa/cibuildwheel v2.11.4 composite
pypa/gh-action-pypi-publish v1.6.4 composite

ci/requirements-viz.txt pypi

ase *
dill >=0.3.2
matplotlib *
pandas *
pathos *
plotly *
scikit-image *
tqdm *
xarray >=0.10.0

ci/requirements.txt pypi

coveralls *
pytest *
pytest-cov *
pytest-env *
pytest-faulthandler *

.github/workflows/codeql/config.yml actions