pynucastro

pynucastro: an interface to nuclear reaction rates and code generator for reaction network equations - Published in JOSS (2018)

https://github.com/pynucastro/pynucastro

Science Score: 100.0%

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
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.zenodo.json file
Found .zenodo.json file
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DOI references
Found 7 DOI reference(s) in README and JOSS metadata
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Academic publication links
Links to: joss.theoj.org, zenodo.org
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5 of 20 committers (25.0%) from academic institutions
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JOSS paper metadata
Published in Journal of Open Source Software

Keywords from Contributors

amrex astrophysical-simulation pde reactions radiation hydrodynamics gravity cfd castro astrophysics

Scientific Fields

Mathematics Computer Science - 72% confidence

Last synced: 4 months ago · JSON representation ·

Repository

a python library for nuclear astrophysics

Basic Info

Host: GitHub
Owner: pynucastro
License: bsd-3-clause
Language: Python
Default Branch: main
Homepage: https://pynucastro.github.io/
Size: 178 MB

Statistics

Stars: 63
Watchers: 2
Forks: 38
Open Issues: 74
Releases: 19

Created about 10 years ago · Last pushed 4 months ago

Metadata Files

Readme Changelog Contributing License Code of conduct Citation Codemeta Zenodo

pynucastro

pynucastro is a python library for nuclear astrophysics. It provides access to nuclear data and reaction rates, and tools for building and interactively exploring nuclear reaction networks.

The main features are:

Easy access to nuclear properties, including T-dependent partition functions, spins, masses, etc.
The ability to create a reaction network based on a collection of rates, a set of nuclei, or an arbitrary filter applied to a library.
- Includes support for ReacLib rates and tabulated weak rates from a variety of sources.
Interactive exploration of rates and networks in Jupyter notebooks, including:
- Many different ways of visualizing a network.
- The ability to export a NetworkX graph (for instance, to find cycles).
Methods to determine which rates are important and which might be missing from a network, as well as analyze the stiffness of a network.
The ability to approximate rates and derive reverse rates via detailed balance.
An NSE solver to find the equilibrium abundance of a set of nuclei given a thermodynamic state.
The ability to write out python or C++ code needed to integrate the network.
Additional physics methods for thermal neutrino sources and Fermi-Dirac integrals.

Documentation

Documentation for pynucastro is available here:

https://pynucastro.github.io/pynucastro/

Examples

Exploring a reaction rate

The following example reads in the ReacLib rate database and gets the rate for C13(p,g)N14 and evaluates it at a temperature of 1.e9 K and makes a plot of the T dependence:

``` In 1: import pynucastro as pyna

In 2: rl = pyna.ReacLibLibrary()

In 3: c13pg = rl.getrateby_name("c13(p,g)n14")

In [4]: c13pg.eval(1.e9) Out[4]: 3883.4778216250666

In [5]: fig = c13pg.plot()

In [6]: fig.savefig("c13pg.png")

```

The resulting figure is:

Creating a network

The following builds a simple network that has carbon burning, outputs the value of the rates at a set of thermodynamic conditions, and plots the network:

``` In 1: import pynucastro as pyna

In 2: nuclei = ["p", "he4", "c12", "n13", "o16", "ne20", "na23", "mg24"]

In 3: net = pyna.networkhelper(nuclei, usetabular_rates=False) modifying N13 ⟶ p + C12 from C12 + p ⟶ N13 + 𝛾 modifying O16 ⟶ He4 + C12 from C12 + He4 ⟶ O16 + 𝛾 modifying Ne20 ⟶ He4 + O16 from O16 + He4 ⟶ Ne20 + 𝛾 modifying Mg24 ⟶ p + Na23 from Na23 + p ⟶ Mg24 + 𝛾 modifying Mg24 ⟶ He4 + Ne20 from Ne20 + He4 ⟶ Mg24 + 𝛾 modifying C12 ⟶ 3 He4 from 3 He4 ⟶ C12 + 𝛾 modifying O16 + p ⟶ He4 + N13 from N13 + He4 ⟶ p + O16 modifying Ne20 + He4 ⟶ p + Na23 from Na23 + p ⟶ He4 + Ne20 modifying Ne20 + He4 ⟶ C12 + C12 from C12 + C12 ⟶ He4 + Ne20 modifying Na23 + p ⟶ C12 + C12 from C12 + C12 ⟶ p + Na23 modifying Mg24 + He4 ⟶ C12 + O16 from O16 + C12 ⟶ He4 + Mg24

In [4]: rho = 1.e7

In [5]: T = 3.e9

In [6]: comp = pyna.Composition(nuclei)

In [7]: comp.set_equal()

In [8]: net.evaluate_rates(rho=rho, T=T, composition=comp) Out[8]: {C12 + p ⟶ N13 + 𝛾: 52860361.23712939, C12 + He4 ⟶ O16 + 𝛾: 231.46132999413808, O16 + He4 ⟶ Ne20 + 𝛾: 4660.126437920582, Ne20 + He4 ⟶ Mg24 + 𝛾: 53650.76987097864, Na23 + p ⟶ Mg24 + 𝛾: 71891152.99067408, C12 + C12 ⟶ p + Na23: 209.07753161235584, C12 + C12 ⟶ He4 + Ne20: 259.65215046037304, N13 + He4 ⟶ p + O16: 355698292.6571981, O16 + C12 ⟶ He4 + Mg24: 0.8082923986833515, Na23 + p ⟶ He4 + Ne20: 6840366554.79809, 3 He4 ⟶ C12 + 𝛾: 0.12389170353139083, N13 ⟶ p + C12: 984313528.3619095, O16 ⟶ He4 + C12: 0.00013799339351820605, Ne20 ⟶ He4 + O16: 39.38899256329942, Mg24 ⟶ p + Na23: 6.121492897494776e-07, Mg24 ⟶ He4 + Ne20: 9.835129431742516e-06, C12 ⟶ 3 He4: 0.008264918834094248, O16 + p ⟶ He4 + N13: 11.428884290229457, Ne20 + He4 ⟶ p + Na23: 317753.8001151714, Ne20 + He4 ⟶ C12 + C12: 1.929507593099608e-05, Na23 + p ⟶ C12 + C12: 0.33819870621531356, Mg24 + He4 ⟶ C12 + O16: 1.8802924022864885e-11}

In [9]: fig = net.plot(rotated=True, hide_xalpha=True)

In [10]: fig.savefig("c-net.png") ```

After the network is created, we see messages saying that a number of reverse rates were rederived using detailed balance.

The resulting figure is:

Interactive exploration

We can also interactively explore a reaction network. Here's an example of hot-CNO with breakout reactions:

by increasing the temperature, you can see the transition from CNO to hot-CNO (proton captures on C13 become faster than the beta decay) and then the breakout of hot-CNO when the alpha capture on O14 becomes faster than its decay.

Installation

pynucastro is available on PyPI and can be installed via: pip install pynucastro

Alternately, to install via source, you can do: pip install . for a systemwide install, or pip install --user . for a single-user install. This will put the pynucastro modules and library in the default location python searches for packages.

Requirements

pynucastro is supported on Python 3.10 or later and the following libraries:

numpy
sympy
scipy
matplotlib
networkx
ipywidgets
numba

To build the documentation or run the unit tests, sphinx and pytest are additionally required along with some supporting packages. See the included requirements.txt file for a list of these packages and versions. To install the packages from the requirements file, do: pip install -r requirements.txt Is important to stress out that all the dependencies should be installed before pynucastro, otherwise the installation should be repeated.

Contributing

We welcome contributions from anyone, including posting issues or submitting pull requests to the pynucastro github. For more details on how to contribute to pynucastro, please see CONTRIBUTING.md.

Core Developers

People who make a number of substantive contributions (new features, bug fixes, etc.) will be named "core developers" of pynucastro.

Core developers will be recognized in the following ways:

invited to the group's slack team
listed in the User's Guide and website as a core developer
listed in the author list on the Zenodo DOI for the project (as given in the .zenodo.json file)
invited to co-author general code papers / proceedings describing pynucastro. (Note: science papers that use pynucastro will always be left to the science paper lead author to determine authorship).

If a core developer is inactive for 3 years, we may reassess their status as a core developer.

Getting Help

We use our Github Discussions page for requesting help and interacting with the community.

Owner

Name: pynucastro
Login: pynucastro
Kind: organization

Repositories: 2
Profile: https://github.com/pynucastro

a python library for nuclear astrophysics

JOSS Publication

pynucastro: an interface to nuclear reaction rates and code generator for reaction network equations

Published

March 18, 2018

DOI

10.21105/joss.00588

Volume 3, Issue 23, Page 588

Authors

Donald E. Willcox

Department of Physics and Astronomy, Stony Brook University

Michael Zingale

Department of Physics and Astronomy, Stony Brook University

Editor

Kathryn Huff

Citation (CITATION.md)

If you use pynucastro, please CITE the "2.0" paper _and_ the latest
Zenodo DOI.  You can also cite the JOSS paper.


## Astrophysical Journal ("2.0 paper")

https://iopscience.iop.org/article/10.3847/1538-4357/acbaff


```bibtex
@ARTICLE{pynucastro2,
doi = {10.3847/1538-4357/acbaff},
url = {https://dx.doi.org/10.3847/1538-4357/acbaff},
year = {2023},
month = {apr},
publisher = {The American Astronomical Society},
volume = {947},
number = {2},
pages = {65},
author = {Alexander I. Smith and Eric T. Johnson and Zhi Chen and
          Kiran Eiden and Donald E. Willcox and Brendan Boyd and
          Lyra Cao and Christopher J. DeGrendele and Michael Zingale},
title = {pynucastro: A Python Library for Nuclear Astrophysics},
journal = {The Astrophysical Journal},
abstract = {We describe pynucastro 2.0, an open-source library for
            interactively creating and exploring astrophysical nuclear
            reaction networks.  We demonstrate new methods for
            approximating rates and use detailed balance to create
            reverse rates, show how to build networks and determine
            whether they are appropriate for a particular science application,
            and discuss the changes made to the library over the past few
            years. Finally, we demonstrate the validity of the networks
            produced and share how we use pynucastro networks in simulation
            codes.}
}
```


## JOSS

https://joss.theoj.org/papers/10.21105/joss.00588

```bibtex
@article{pynucastro,
   author = {{Willcox}, D.~E. and {Zingale}, M.},
    title = "{pynucastro: an interface to nuclear reaction rates and code generator for reaction network equations}",
  journal = {Journal of Open Source Software},
     year = 2018,
   volume = 3,
   number = 23,
   pages = 588,
     url = {https://doi.org/10.21105/joss.00588},
     doi = {10.21105/joss.00588},
 subject = {nuclear astrophysics}
}
```

## Zenodo

The Zenodo record is:
https://doi.org/10.5281/zenodo.1202434

CodeMeta (codemeta.json)

{
  "@context": "https://raw.githubusercontent.com/codemeta/codemeta/main/codemeta.jsonld",
  "@type": "Code",
  "author": [
    {
      "@id": " https://orcid.org/0000-0003-2300-5165",
      "@type": "Person",
      "email": "donald.willcox@stonybrook.edu",
      "name": "Donald E. Willcox",
      "affiliation": "Department of Physics and Astronomy, Stony Brook University"
    },
    {
      "@id": "https://orcid.org/0000-0001-8401-030X",
      "@type": "Person",
      "email": "michael.zingale@stonybrook.edu",
      "name": "Michael Zingale",
      "affiliation": "Department of Physics and Astronomy, Stony Brook University"
    }
  ],
  "identifier": "",
  "codeRepository": "https://github.com/pynucastro/pynucastro",
  "datePublished": "2018-01-29",
  "dateModified": "2018-01-29",
  "dateCreated": "2018-01-29",
  "description": "pynucastro is an interface to nuclear reaction rates and code generator for reaction network equations.",
  "keywords": "nuclear, reactions, astrophysics, physics, visualization, code generation, integration, differential equations",
  "license": "BSD",
  "title": "pynucastro",
  "version": "1.0.0"
}

GitHub Events

Total

Create event: 18
Release event: 2
Issues event: 71
Watch event: 8
Delete event: 17
Issue comment event: 247
Push event: 332
Pull request review comment event: 141
Pull request event: 345
Pull request review event: 297
Fork event: 4

Last Year

Create event: 19
Release event: 2
Issues event: 71
Watch event: 8
Delete event: 17
Issue comment event: 247
Push event: 332
Pull request review comment event: 141
Pull request event: 347
Pull request review event: 297
Fork event: 4

Committers

Last synced: 5 months ago

All Time

Total Commits: 1,390
Total Committers: 20
Avg Commits per committer: 69.5
Development Distribution Score (DDS): 0.454

Past Year

Commits: 233
Committers: 7
Avg Commits per committer: 33.286
Development Distribution Score (DDS): 0.142

Top Committers

Name	Email	Commits
Michael Zingale	m**e@s**u	759
Donald E. Willcox	e**x@g**m	391
Eric T. Johnson	e**n@s**u	114
Zhi Chen	6****3	34
Alexander Smith Clark	a**k@s**u	26
Kiran Eiden	k**n@g**m	15
Brendan Boyd	4****d	15
SamG-01	1****1	7
dependabot[bot]	4****]	5
Max Katz	m**z@g**m	5
Adam M. Jacobs	a**s@p**u	5
Josiah Schwab	j**b@g**m	4
Travis CI User	t**s@e**g	2
Chris DeGrendele	3****e	2
alecpwills	a**s@s**u	1
Abigail Bishop	m**p@g**m	1
Lyra Cao	c**a@g**m	1
Parker-T-Johnson	1****n	1
XinlongSBU	4****U	1
hansbdein	1****n	1

Committer Domains (Top 20 + Academic)

stonybrook.edu: 4 example.org: 1 pa.msu.edu: 1

Issues and Pull Requests

Last synced: 4 months ago

All Time

Total issues: 139
Total pull requests: 764
Average time to close issues: 10 months
Average time to close pull requests: 11 days
Total issue authors: 14
Total pull request authors: 13
Average comments per issue: 1.11
Average comments per pull request: 0.96
Merged pull requests: 615
Bot issues: 0
Bot pull requests: 13

Past Year

Issues: 60
Pull requests: 447
Average time to close issues: 26 days
Average time to close pull requests: 10 days
Issue authors: 8
Pull request authors: 7
Average comments per issue: 0.7
Average comments per pull request: 0.87
Merged pull requests: 336
Bot issues: 0
Bot pull requests: 3

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Top Authors

Issue Authors

zingale (111)
dwillcox (7)
hansbdein (3)
yut23 (3)
aisclark91 (3)
rat1402 (3)
arkabratagupta (2)
zhichen3 (1)
Chirashree-India (1)
DHasenour (1)
sameulleaf (1)
SamG-01 (1)
azniaa (1)
qmichalski (1)

Pull Request Authors

zingale (536)
yut23 (116)
aisclark91 (32)
zhichen3 (30)
dependabot[bot] (13)
SamG-01 (12)
KiranEiden (8)
biboyd (7)
ethanstony (3)
maxpkatz (2)
brady-ryan (2)
Parker-T-Johnson (2)
hansbdein (1)

Top Labels

Issue Labels

enhancement (23) weak rates (12) nuclear data (10) documentation (10) networks (9) design (7) C++ generation (5) bug (4) plotting (3) help wanted (3) python nets (3) reaclib rates (2) examples (2) custom rate (1)

Pull Request Labels

documentation (122) enhancement (27) C++ generation (19) networks (17) design (16) plotting (15) dependencies (14) weak rates (13) EOS (11) testing (8) nuclear data (6) python (6) github_actions (5) examples (3) reaclib rates (3) approximate rates (2) bug (2) python nets (1)

Packages

Total packages: 1
Total downloads:
- pypi 197 last-month

Total dependent packages: 0
Total dependent repositories: 1
Total versions: 14
Total maintainers: 2

pypi.org: pynucastro

A python library for nuclear astrophysics

Homepage: https://github.com/pynucastro/pynucastro
Documentation: https://pynucastro.github.io/pynucastro/
License: BSD
Latest release: 2.7.1
published 5 months ago

Versions: 14
Dependent Packages: 0
Dependent Repositories: 1
Downloads: 197 Last month

Rankings

Forks count: 7.6%

Stargazers count: 9.5%

Dependent packages count: 10.1%

Average: 14.0%

Downloads: 21.4%

Dependent repos count: 21.6%

Maintainers (2)

yut23 zingale

Last synced: 4 months ago

Dependencies

requirements.txt pypi

Sphinx *
ipywidgets >=7.1.2
jinja2 ==3.0.3
jupyter >=1.0.0
matplotlib >=2.1.0
nbsphinx >=0.3.1
nbval >=0.9.0
networkx >=2.1
numba >=0.40
numpy >=1.13.3
pytest >=3.6
pytest-cov >=2.6.0
scipy >=1.0.0
setuptools_scm >=6.2
sphinx_rtd_theme *
sympy >=1.1.1

setup.py pypi

ipywidgets *
matplotlib *
networkx *
numpy *
scipy *
sympy *

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pynucastro

Science Score: 100.0%

Keywords from Contributors

Scientific Fields

Repository

Basic Info

Statistics

Metadata Files

README.md

pynucastro

Documentation

Examples

Exploring a reaction rate

Creating a network

Interactive exploration

Installation

Requirements

Contributing

Core Developers

Getting Help

Owner

JOSS Publication

pynucastro: an interface to nuclear reaction rates and code generator for reaction network equations

Authors

Editor

Tags

Citation (CITATION.md)

CodeMeta (codemeta.json)

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Packages

pypi.org: pynucastro

Rankings

Maintainers (2)

Dependencies