.. starmatrix
.. |ci-badge| image:: https://github.com/xuanxu/starmatrix/actions/workflows/tests.yml/badge.svg :target: https://github.com/xuanxu/starmatrix/actions/workflows/tests.yml :alt: Build status .. |docs-badge| image:: https://readthedocs.org/projects/starmatrix/badge/?version=latest :target: https://starmatrix.readthedocs.io/en/latest/?badge=latest :alt: Documentation Status .. |codecov-badge| image:: https://codecov.io/gh/xuanxu/starmatrix/branch/main/graph/badge.svg?token=JRNGFn3SjA :target: https://codecov.io/gh/xuanxu/starmatrix :alt: Coverage status .. |license| image:: https://img.shields.io/github/license/xuanxu/starmatrix?color=brightgreen :target: https://github.com/xuanxu/starmatrix/blob/main/LICENSE :alt: MIT License .. |version| image:: https://img.shields.io/pypi/v/starmatrix.svg?color=brightgreen :target: https://pypi.org/project/starmatrix/ :alt: starmatrix in PyPi .. |paper-link| image:: https://joss.theoj.org/papers/10.21105/joss.04461/status.svg :target: https://doi.org/10.21105/joss.04461 :alt: Paper
|ci-badge| |docs-badge| |codecov-badge| |license| |version| |paper-link|
Starmatrix is a Q-Matrices generator.
Based on explicit values for solar abundances, Z and IMF, Starmatrix calculates matrices Q(i,j) of masses of elements i ejected to the galactic medium as element j, for a complete range of stellar masses, accounting for supernovae of types Ia and II. You can read more about the Matrices Q formalism in Ferrini et al. 1992.
Starmatrix computes the contribution matrix of 15 elements:
= = === === = === = = ==== == == == = == == H D He3 He4 C C13 N O n.r. Ne Mg Si S Ca Fe = = === === = === = = ==== == == == = == ==
Starmatrix is a tool for astronomers working with galactic chemical evolution models needing detailed datasets to use as input, wanting to compare the validity of different yield sets or assessing different nucleosynthesis modeling assumptions.
The easiest way to install the package is using pip::
$ pip install starmatrixThis will install the most recent release version and also some dependencies if they are not found in the system: numpy, scipy and pyyaml
A previous installation can be upgraded to the latest version with::
$ pip install --upgrade starmatrixIf you want to play with the latest code present in this repository even if it has not been released yet, you can do it by cloning the repo locally and instructing pip to install it::
$ git clone https://github.com/xuanxu/starmatrix.git
$ cd starmatrix
$ pip install -e .Python >= 3.7 is required.
To test installation worked you can just run Starmatrix with default values running::
$ starmatrix --generate-config
$ starmatrix --config config-example.ymlThe first command will generate a basic configuration file (named config-example.yml) and the second command will run Starmatrix using that configuration. A folder named results should be created with the output files.
Starmatrix includes a test suite located in the /src/starmatrix/tests directory. The current state of the build is publicly tracked by GitHub CI_. You can run the latest tests locally and get information on code coverage if you clone the code to your local machine, install its development dependencies and use pytest::
$ git clone https://github.com/xuanxu/starmatrix.git
$ cd starmatrix
$ pip install -e ".[dev]"
$ pytest.. _publicly tracked by GitHub CI: https://github.com/xuanxu/starmatrix/actions/workflows/tests.yml
Use starmatrix running::
$ starmatrix --config FILENAMEwhere FILENAME is the path to the config yaml file.
Running starmatrix will produce a directory with three output files:
You can find the complete documentation at ReadTheDocs' Starmatrix page_.
.. _ReadTheDocs' Starmatrix page: https://starmatrix.readthedocs.io/
Starmatrix reads a config file where several options can be set in yaml format::
z: 0.0200 # metallicity
sol_ab: as09 # solar abundances
imf: kroupa2002 # initial mass function (IMF)
imf_m_low: 0.15 # lower mass limit for the IMF
imf_m_up: 100 # upper mass limit for the IMF
total_time_steps: 300 # number of time steps (will result in a Q Matrix per step)
m_min: 0.98 # min value for stellar mass
m_max: 40 # max value for stellar mass
binary_fraction: 0.15 # rate of binary stars
snia_m_max # Upper mass limit for binaries with SN Ia. Default value: 16 Msun
dtd_sn: rlp # delay time distribution for supernovae
sn_yields: iwa1998 # Dataset for Supernovae yields
output_dir: results # Name of the directory where results are written.
integration_step: logt # The integration step can be constant in t, constant in log(t), or custom.
expelled_elements_filename: ejecta.txt # Filename of ejected data.Starmatrix will use its internal default values_ for all params for which no values are provided.
If you want to use an existent configuration file as template for your own, you can run::
$ starmatrix --generate-configThat command will create a config-example.yml file in the current dir containing the default values.
.. _default values: https://starmatrix.readthedocs.io/en/latest/configuration.html#default-values
Starmatrix uses solar mass (M) as the reference unit for all quantities, so internally the upper and lower limits for IMF are expressed in solar masses, Delay Time Distributions are expressed as [Supernovae per Year per M] and the expelled elements file is expected to express data as expelled mass per solar mass, same as the supernova yields.
The imf param in the config file can be set to use any of the predefined IMFs from different papers/authors:
:salpeter: Salpeter 1955 :starburst: Starburst 1999 (a Salpeter with mass limits in [1, 120]) :miller_scalo: Miller & Scalo 1979 :ferrini: Ferrini, Palla & Penco 1998 :kroupa2001: Kroupa 2001 :kroupa2002: Kroupa 2002 :chabrier: Chabrier 2003 :maschberger: Maschberger 2012
The default value is kroupa2002. If you want to use your own IMF you can do so subclassing the IMF class_.
.. _IMF class: https://github.com/xuanxu/starmatrix/blob/main/src/starmatrix/imfs.py#L35-L68
The IMF will be normalized integrating in the [imf_m_low, imf_m_up] mass interval (default: [0.15, 100], except Starburst: [1, 120]).
The sol_ab param in the config file can be set to use any of the available abundances datasets from different papers/authors:
:ag89: Anders & Grevesse 1989 :gs98: Grevesse & Sauval 1998 :as05: Asplund et al. 2005 :as09: Asplund et al. 2009 :he10: Heger 2010 :lo19: Lodders et al. 2019
The default value is as09. If you want to use your own abundances data you can do so subclassing the Abundances class_.
.. _Abundances class: https://github.com/xuanxu/starmatrix/blob/main/src/starmatrix/abundances.py#L30-L59
The dtd_sn param in the config file can be set to use any of the available Delay Time Distributions for supernova rates from different papers/authors:
:rlp: Supernova rates from Ruiz-Lapuente et al. (2000) :maoz: DTD of Type Ia supernovae from Maoz & Graur (2017) :castrillo: DTD of Type Ia supernovae from Castrillo et al. (2021) :greggio: DTD of Type Ia supernovae from Greggio, L. (2005) :chen: DTD of Type Ia supernovae from Chen et al. (2021) :greggio-CDD04: DTD from model Close DD 0.4 Gyrs from Greggio, L. (2005) :greggio-CDD1: DTD from model Close DD 1 Gyr from Greggio, L. (2005) :greggio-WDD04: DTD from model Wide DD 0.4 Gyrs from Greggio, L. (2005) :greggio-WDD1: DTD from model Wide DD 1 Gyr from Greggio, L. (2005) :greggio-SDCH: DTD from model SD Chandra from Greggio, L. (2005) :greggio-SDSCH: DTD from model SD sub-Chandra from Greggio, L. (2005) :strolger-fit1: Phi function from Strolger et al. (2020) with (ξ, ω, 𝛼) = (10, 600, 220) :strolger-fit2: Phi function from Strolger et al. (2020) with (ξ, ω, 𝛼) = (110, 1000, 2) :strolger-fit3: Phi function from Strolger et al. (2020) with (ξ, ω, 𝛼) = (350, 1200, 20) :strolger-fit4: Phi function from Strolger et al. (2020) with (ξ, ω, 𝛼) = (6000, 6000, -2) :strolger-fit5: Phi function from Strolger et al. (2020) with (ξ, ω, 𝛼) = (-650, 2200, 1100) :strolger-optimized: Phi function from Strolger et al. (2020) with (ξ, ω, 𝛼) = (-1518, 51, 50)
The sn_yields param in the config file can be set to use any of the available supernova yields datasets from different papers/authors:
:iwa1998: Data from Iwamoto, K. et al., 1999 :sei2013: Data from Seitenzahl et al. 2013 :ln2018-1: Data from Leung & Nomoto 2018, Tables 6/7 :ln2018-2: Data from Leung & Nomoto 2018, Tables 8/9 :ln2018-3: Data from Leung & Nomoto 2018, Tables 10/11 :ln2020: Data from Leung & Nomoto 2020 :br2019-1: Data from Bravo, E. et al., Table 3 :br2019-2: Data from Bravo, E. et al., Table 4 :gro2021-1: Data from Gronow, S. et al., Tables 3/A10 He+Core detonations :gro2021-2: Data from Gronow, S. et al., Tables 4/A8 He+Core detonations :mor2018-1: Data from Mori, K. et al., W7 :mor2018-2: Data from Mori, K. et al., WDD2
If you find a bug or have a question, please open an issue in the project's repo.
Contributions are welcome, please read our contributing guidelines_.
.. _contributing guidelines: https://github.com/xuanxu/starmatrix/blob/main/CONTRIBUTING.md
If you find Starmatrix helpful, please consider citing:
::
@article{Bazan2022, doi = {10.21105/joss.04461}, url = {https://doi.org/10.21105/joss.04461}, year = {2022}, publisher = {The Open Journal}, volume = {7}, number = {75}, pages = {4461}, author = {Juanjo Bazán and Mercedes Mollá}, title = {Starmatrix: Modelling nucleosynthesis of galactic chemical elements}, journal = {Journal of Open Source Software} }
Copyright © Juanjo Bazán, released under the MIT license_.
.. _MIT license: https://github.com/xuanxu/starmatrix/blob/main/LICENSE
Starmatrix is built upon a long list of previous works from different authors/papers: