21cmFAST v3

21cmFAST v3: A Python-integrated C code for generating 3D realizations of the cosmic 21cm signal. - Published in JOSS (2020)

https://github.com/21cmfast/21cmfast

Science Score: 95.0%

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

○
CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
✓
.zenodo.json file
Found .zenodo.json file
✓
DOI references
Found 15 DOI reference(s) in README and JOSS metadata
✓
Academic publication links
Links to: joss.theoj.org
✓
Committers with academic emails
3 of 28 committers (10.7%) from academic institutions
○
Institutional organization owner
✓
JOSS paper metadata
Published in Journal of Open Source Software

Keywords from Contributors

exoplanet mesh energy-system gravitational-lensing hydrology gaussian-processes exoplanet-radial-velocities exoplanet-transits mcmc pymc3

Scientific Fields

Mathematics Computer Science - 84% confidence

Last synced: 4 months ago · JSON representation

Repository

Official repository for 21cmFAST: a code for generating fast simulations of the cosmological 21cm signal

Basic Info

Host: GitHub
Owner: 21cmfast
License: mit
Language: C
Default Branch: main
Size: 103 MB

Statistics

Stars: 66
Watchers: 7
Forks: 43
Open Issues: 74
Releases: 1

Created over 6 years ago · Last pushed 5 months ago

Metadata Files

Readme Changelog Contributing License Authors

README.rst

========
21cmFAST
========

.. start-badges
.. image:: https://travis-ci.org/21cmFAST/21cmFAST.svg
    :target: https://travis-ci.org/21cmFAST/21cmFAST
.. image:: https://coveralls.io/repos/github/21cmFAST/21cmFAST/badge.svg
    :target: https://coveralls.io/github/21cmFAST/21cmFAST
.. image:: https://img.shields.io/badge/code%20style-black-000000.svg
    :target: https://github.com/ambv/black
.. image:: https://readthedocs.org/projects/21cmfast/badge/?version=latest
    :target: https://21cmfast.readthedocs.io/en/latest/?badge=latest
    :alt: Documentation Status
.. image:: https://img.shields.io/conda/dn/conda-forge/21cmFAST
    :target: https://github.com/conda-forge/21cmfast-feedstock
    :alt: Conda
.. image:: https://joss.theoj.org/papers/10.21105/joss.02582/status.svg
   :target: https://doi.org/10.21105/joss.02582
.. end-badges

**A semi-numerical cosmological simulation code for the radio 21-cm signal.**

.. image:: joss-paper/yuxiangs-plot-small.png
    :target: http://homepage.sns.it/mesinger/Media/lightcones_minihalo.png


This is the official repository for ``21cmFAST``: a semi-numerical code that is able to
produce 3D cosmological realisations of many physical fields in the early Universe.
It is super-fast, combining the excursion set formalism with perturbation theory to
efficiently generate density, velocity, halo, ionization, spin temperature, 21-cm, and
even ionizing flux fields (see the above lightcones!).
It has been tested extensively against numerical simulations, with excellent agreement
at the relevant scales.

``21cmFAST`` has been widely used, for example, by the Murchison Widefield Array (MWA),
LOw-Frequency ARray (LOFAR) and Hydrogen Epoch of Reionization Array (HERA), to model the
large-scale cosmological 21-cm signal. In particular, the speed of ``21cmFAST`` is important
to produce simulations that are large enough (several Gpc across) to represent modern
low-frequency observations.

Documentation
=============
Full documentation (with examples, installation instructions and full API reference)
found at https://21cmfast.readthedocs.org.

New Features in 4.0.0
=====================

* A discrete halo sampler allowing for the creation of lightcones of galaxy properties and the
  inclusion of stochasticity. These discrete sources are self-consistently used in the IGM calculations
* The Inclusion of the Sheth-Tormen conditional halo mass function.
* Re-designed input/output structures which prioritise transparency.
* Refactoring of several of the C backend files for much easier development.
* A lower-level testing framework for calculations done in the backend.

As of ``v3.0.0``, ``21cmFAST`` is conveniently wrapped in Python to enable more dynamic code.


New Features in 3.0.0+
======================

* Robust on-disk caching/writing both for efficiency and simplified reading of
  previously processed data (using HDF5).
* Convenient data objects which simplify access to and processing of the various density
  and ionization fields.
* De-coupled functions mean that arbitrary functionality can be injected into the process.
* Improved exception handling and debugging
* Comprehensive documentation
* Comprehensive test suite.
* Strict `semantic versioning `_.


Installation
============
We support Linux and MacOS (please let us know if you are successful in installing on
Windows!). On these systems, the simplest way to get ``21cmFAST`` is by using
`conda `_::

    conda install -c conda-forge 21cmFAST

``21cmFAST`` is also available on PyPI, so that ``pip install 21cmFAST`` also works. However,
it depends on some external (non-python) libraries that may not be present, and so this
method is discouraged unless absolutely necessary. If using ``pip`` to install ``21cmFAST``
(especially on MacOS), we thoroughly recommend reading the detailed
`installation instructions `_.



Acknowledging
=============
If you use ``21cmFAST v3+`` in your research please cite both of:

    Murray et al., (2020). 21cmFAST v3: A Python-integrated C code for generating 3D
    realizations of the cosmic 21cm signal. Journal of Open Source Software, 5(54),
    2582, https://doi.org/10.21105/joss.02582

    Andrei Mesinger, Steven Furlanetto and Renyue Cen, "21CMFAST: a fast, seminumerical
    simulation of the high-redshift 21-cm signal", Monthly Notices of the Royal
    Astronomical Society, Volume 411, Issue 2, pp. 955-972 (2011),
    https://ui.adsabs.harvard.edu/link_gateway/2011MNRAS.411..955M/doi:10.1111/j.1365-2966.2010.17731.x

In addition, the following papers introduce various features into ``21cmFAST``. If you use
these features, please cite the relevant papers.

Discrete Halo Sampler / version 4:

    Davies, J. E., Mesinger, A., Murray, S. G.,
    "Efficient simulation of discrete galaxy populations and associated radiation fields during the first billion years",
    eprint arXiv:2504.17254, 2025. https://doi.org/10.48550/arXiv.2504.17254

Mini-halos:

    Muñoz, J.B., Qin, Y., Mesinger, A., Murray, S., Greig, B., and Mason, C.,
    "The Impact of the First Galaxies on Cosmic Dawn and Reionization",
    Monthly Notices of the Royal Astronomical Society, vol. 511, no. 3,
    pp 3657-3681, 2022 https://doi.org/10.1093/mnras/stac185
    (for DM-baryon relative velocities)

    Qin, Y., Mesinger, A., Park, J., Greig, B., and Muñoz, J. B.,
    “A tale of two sites - I. Inferring the properties of minihalo-hosted galaxies from
    current observations”, Monthly Notices of the Royal Astronomical Society, vol. 495,
    no. 1, pp. 123–140, 2020. https://doi.org/10.1093/mnras/staa1131.
    (for Lyman-Werner and first implementation)

Mass-dependent ionizing efficiency:

    Park, J., Mesinger, A., Greig, B., and Gillet, N.,
    “Inferring the astrophysics of reionization and cosmic dawn from galaxy luminosity
    functions and the 21-cm signal”, Monthly Notices of the Royal Astronomical Society,
    vol. 484, no. 1, pp. 933–949, 2019. https://doi.org/10.1093/mnras/stz032.

If you are unsure which modules are used within your simulations, we provide a handy function
to print out which works to refer ``py21cmfast.utils.show_references``, which accepts a single instance of
the ``InputParameters`` class and shows which papers are relevant for your simulation.

Owner

Name: 21cmFAST Collaboration
Login: 21cmfast
Kind: organization
Email: 21cmfast.coredev@gmail.com

Repositories: 3
Profile: https://github.com/21cmfast

Core team that develops 21cmFAST and associated packages

JOSS Publication

21cmFAST v3: A Python-integrated C code for generating 3D realizations of the cosmic 21cm signal.

Published

October 22, 2020

DOI

10.21105/joss.02582

Volume 5, Issue 54, Page 2582

Authors

Steven G. Murray

School of Earth and Space Exploration, Arizona State University, Phoenix, USA

Bradley Greig

ARC Centre of Excellence for All-Sky Astrophysics in 3 Dimensions (ASTRO 3D), School of Physics, University of Melbourne, Parkville, VIC 3010, Australia

Andrei Mesinger

Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy

Julian B. Muñoz

Department of Physics, Harvard University, 17 Oxford St., Cambridge, MA, 02138, USA

Yuxiang Qin

Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy

Jaehong Park

Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy, School of Physics, Korea Institute for Advanced Study, 85 Hoegiro, Dongdaemun-gu, Seoul, 02455, Republic of Korea

Catherine A. Watkinson

School of Physics and Astronomy, Queen Mary University of London, G O Jones Building, 327 Mile End Road, London, E1 4NS, UK

Editor

Dan Foreman-Mackey

GitHub Events

Total

Issues event: 39
Watch event: 7
Delete event: 72
Issue comment event: 183
Push event: 466
Pull request event: 154
Pull request review event: 300
Pull request review comment event: 256
Fork event: 4
Create event: 90

Last Year

Issues event: 41
Watch event: 7
Delete event: 72
Issue comment event: 186
Push event: 469
Pull request event: 156
Pull request review event: 302
Pull request review comment event: 257
Fork event: 4
Create event: 91

Committers

Last synced: 5 months ago

All Time

Total Commits: 2,409
Total Committers: 28
Avg Commits per committer: 86.036
Development Distribution Score (DDS): 0.607

Past Year

Commits: 637
Committers: 15
Avg Commits per committer: 42.467
Development Distribution Score (DDS): 0.411

Top Committers

Name	Email	Commits
Steven Murray	s**y@c**u	947
James Davies	j**s@s**t	648
BradGreig	b**g@s**u	343
Yuxiang Qin	Y**n@g**m	106
pre-commit-ci[bot]	6****]	99
Jordan Flitter	j**r@J**l	63
Yuxiang Qin	y**n@s**t	60
JulianBMunoz	j**r@g**m	55
debanjan-cosmo	8****o	23
DanielaBreitman	d**n@m**a	13
Jaehong Park	j**k@J**l	8
Jordan Flitter	y**r@g**m	6
James Davies	j**s@t**t	5
Charlotte Mason	c**m@g**m	4
dependabot[bot]	4****]	4
David Prelogovic	d**c@g**m	4
James Edward Davies	j**0@l**l	3
Dan Foreman-Mackey	f**y@g**m	3
Remy Moll	me@m****e	3
raxquax123	1****3	2
Catherine Watkinson	c**n@g**m	2
Jordan Flitter	j**r@J**n	2
catherinewatkinson	c**n@g**m	1
James Davies	d**e@z**t	1
James Edward Davies	j**0@l**l	1
yuxiang qin	y**n@t**t	1
andreimesinger	a**r@s**t	1
Samuel Gagnon-Hartman	s**n@g**m	1

Committer Domains (Top 20 + Academic)

sns.it: 3 trantor01.hpc.sns.it: 2 zifnab.sns.it: 1 jordans-mbp.lan: 1 moll.re: 1 mail.mcgill.ca: 1 student.unimelb.edu.au: 1 curtin.edu.au: 1

Issues and Pull Requests

Last synced: 4 months ago

All Time

Total issues: 134
Total pull requests: 315
Average time to close issues: about 1 year
Average time to close pull requests: about 1 month
Total issue authors: 35
Total pull request authors: 17
Average comments per issue: 2.07
Average comments per pull request: 1.71
Merged pull requests: 232
Bot issues: 0
Bot pull requests: 68

Past Year

Issues: 29
Pull requests: 177
Average time to close issues: about 2 months
Average time to close pull requests: 7 days
Issue authors: 10
Pull request authors: 11
Average comments per issue: 0.24
Average comments per pull request: 1.31
Merged pull requests: 130
Bot issues: 0
Bot pull requests: 32

View more stats

Top Authors

Issue Authors

steven-murray (35)
daviesje (32)
jordanflitter (9)
qyx268 (7)
JasperSolt (6)
BradGreig (5)
andreimesinger (4)
Andresfgomez970 (3)
zhaotingchen (2)
dprelogo (2)
oscarhdz7 (2)
samgagnon (2)
bohuarolandli (2)
SuvedhaNaik (2)
flomertens (1)

Pull Request Authors

daviesje (118)
steven-murray (76)
pre-commit-ci[bot] (58)
jordanflitter (25)
dependabot[bot] (10)
BradGreig (5)
moll-re (4)
DanielaBreitman (3)
raxquax123 (3)
andreimesinger (2)
qyx268 (2)
debanjan-cosmo (2)
samgagnon (2)
JulianBMunoz (2)
charlottenosam (1)

Top Labels

Issue Labels

context: C backend (35) context: python wrapper (29) context: v4-prep (24) type: bug (17) bug (17) type: refactor (13) priority: medium (13) context: cache/io (10) priority: high (9) status: requires discussion (8) question (7) priority: low (7) docs (6) good first issue (6) status: requires research (6) context: installation (6) type: feature: physical (5) API Breaking (4) type: feature: code (4) type: testing (4) type: performance: speed (3) type: ux (3) type: question (3) context: error-handling (2) type: performance: memory (2) type: documentation (2) type: feature: accuracy (2) status: wontfix (1) type: maintenance (1) science project (1)

Pull Request Labels

type: bug (9) auto-pr (7) context: C backend (6) priority: medium (4) context: python wrapper (4) priority: high (3) context: cache/io (2) type: testing (2) bug (2) context: v4-prep (2) type: feature: physical (2) context: installation (1) type: maintenance (1) type: feature: accuracy (1) type: feature: ui (1) type: performance: memory (1) dependencies (1) github_actions (1)

Packages

Total packages: 2
Total downloads:
- pypi 1,103 last-month

Total dependent packages: 4
(may contain duplicates)
Total dependent repositories: 0
(may contain duplicates)
Total versions: 32
Total maintainers: 3

pypi.org: 21cmfast

A semi-numerical cosmological simulation code for the 21cm signal

Homepage: https://github.com/21cmFAST/21cmFAST
Documentation: https://21cmfast.readthedocs.io/
License: MIT license
Latest release: 3.4.0
published over 1 year ago

Versions: 24
Dependent Packages: 4
Dependent Repositories: 0
Downloads: 1,103 Last month

Rankings

Dependent packages count: 2.4%

Forks count: 7.2%

Stargazers count: 9.4%

Downloads: 11.3%

Average: 19.5%

Dependent repos count: 67.1%

Maintainers (3)

stevenjeanette 21cmfast-collaboration daviesje

Last synced: 4 months ago

conda-forge.org: 21cmfast

21cmFAST provides a simple and fast simulation package for the cosmological 21cm signal as either coeval cubes or full lightcones.

Homepage: https://github.com/21cmFAST/21cmFAST
License: MIT
Latest release: 3.2.0
published over 3 years ago

Versions: 8
Dependent Packages: 0
Dependent Repositories: 0

Rankings

Forks count: 33.2%

Dependent repos count: 34.0%

Average: 39.6%

Stargazers count: 39.9%

Dependent packages count: 51.2%

Last synced: 5 months ago

Dependencies

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setup.py pypi

astropy >=2.0
bidict *
cached_property *
cffi >=1.0
click *
h5py >=2.8.0
matplotlib *
numpy *
pyyaml *
scipy *

pyproject.toml pypi

docs/environment.yaml pypi

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nbsphinx *
setuptools_scm *
sphinx-rtd-theme *

21cmFAST v3

Science Score: 95.0%

Keywords from Contributors

Scientific Fields

Repository

Basic Info

Statistics

Metadata Files

README.rst

Owner

JOSS Publication

21cmFAST v3: A Python-integrated C code for generating 3D realizations of the cosmic 21cm signal.

Authors

Editor

Tags

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pypi.org: 21cmfast

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conda-forge.org: 21cmfast

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