From 269ec792a0bef90ea432681b149bb7644ba3b019 Mon Sep 17 00:00:00 2001 From: Wang Boyu Date: Sun, 8 Sep 2024 13:26:52 -0400 Subject: [PATCH] add sample joss paper --- paper/paper.bib | 83 +++++++++++++++++++++++++++++++++ paper/paper.md | 120 ++++++++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 203 insertions(+) create mode 100644 paper/paper.bib create mode 100644 paper/paper.md diff --git a/paper/paper.bib b/paper/paper.bib new file mode 100644 index 0000000..4de9067 --- /dev/null +++ b/paper/paper.bib @@ -0,0 +1,83 @@ + +@article{Pearson:2017, + Adsnote = {Provided by the SAO/NASA Astrophysics Data System}, + Adsurl = {http://adsabs.harvard.edu/abs/2017arXiv170304627P}, + Archiveprefix = {arXiv}, + Author = {{Pearson}, S. and {Price-Whelan}, A.~M. and {Johnston}, K.~V.}, + Eprint = {1703.04627}, + Journal = {ArXiv e-prints}, + Keywords = {Astrophysics - Astrophysics of Galaxies}, + Month = mar, + Title = {{Gaps in Globular Cluster Streams: Pal 5 and the Galactic Bar}}, + Year = 2017} + +@book{Binney:2008, + Adsnote = {Provided by the SAO/NASA Astrophysics Data System}, + Adsurl = {http://adsabs.harvard.edu/abs/2008gady.book.....B}, + Author = {{Binney}, J. and {Tremaine}, S.}, + Booktitle = {Galactic Dynamics: Second Edition, by James Binney and Scott Tremaine.~ISBN 978-0-691-13026-2 (HB).~Published by Princeton University Press, Princeton, NJ USA, 2008.}, + Publisher = {Princeton University Press}, + Title = {{Galactic Dynamics: Second Edition}}, + Year = 2008} + +@article{zenodo, + Abstractnote = {

Gala is a Python package for Galactic astronomy and gravitational dynamics. The bulk of the package centers around implementations of gravitational potentials, numerical integration, and nonlinear dynamics.

}, + Author = {Adrian Price-Whelan and Brigitta Sipocz and Syrtis Major and Semyeong Oh}, + Date-Modified = {2017-08-13 14:14:18 +0000}, + Doi = {10.5281/zenodo.833339}, + Month = {Jul}, + Publisher = {Zenodo}, + Title = {adrn/gala: v0.2.1}, + Year = {2017}, + Bdsk-Url-1 = {http://dx.doi.org/10.5281/zenodo.833339}} + +@ARTICLE{gaia, + author = {{Gaia Collaboration} and {Prusti}, T. and {de Bruijne}, J.~H.~J. and + {Brown}, A.~G.~A. and {Vallenari}, A. and {Babusiaux}, C. and + {Bailer-Jones}, C.~A.~L. and {Bastian}, U. and {Biermann}, M. and + {Evans}, D.~W. and et al.}, + title = "{The Gaia mission}", + journal = {\aap}, +archivePrefix = "arXiv", + eprint = {1609.04153}, + primaryClass = "astro-ph.IM", + keywords = {space vehicles: instruments, Galaxy: structure, astrometry, parallaxes, proper motions, telescopes}, + year = 2016, + month = nov, + volume = 595, + eid = {A1}, + pages = {A1}, + doi = {10.1051/0004-6361/201629272}, + adsurl = {http://adsabs.harvard.edu/abs/2016A%26A...595A...1G}, + adsnote = {Provided by the SAO/NASA Astrophysics Data System} +} + +@ARTICLE{astropy, + author = {{Astropy Collaboration} and {Robitaille}, T.~P. and {Tollerud}, E.~J. and + {Greenfield}, P. and {Droettboom}, M. and {Bray}, E. and {Aldcroft}, T. and + {Davis}, M. and {Ginsburg}, A. and {Price-Whelan}, A.~M. and + {Kerzendorf}, W.~E. and {Conley}, A. and {Crighton}, N. and + {Barbary}, K. and {Muna}, D. and {Ferguson}, H. and {Grollier}, F. and + {Parikh}, M.~M. and {Nair}, P.~H. and {Unther}, H.~M. and {Deil}, C. and + {Woillez}, J. and {Conseil}, S. and {Kramer}, R. and {Turner}, J.~E.~H. and + {Singer}, L. and {Fox}, R. and {Weaver}, B.~A. and {Zabalza}, V. and + {Edwards}, Z.~I. and {Azalee Bostroem}, K. and {Burke}, D.~J. and + {Casey}, A.~R. and {Crawford}, S.~M. and {Dencheva}, N. and + {Ely}, J. and {Jenness}, T. and {Labrie}, K. and {Lim}, P.~L. and + {Pierfederici}, F. and {Pontzen}, A. and {Ptak}, A. and {Refsdal}, B. and + {Servillat}, M. and {Streicher}, O.}, + title = "{Astropy: A community Python package for astronomy}", + journal = {\aap}, +archivePrefix = "arXiv", + eprint = {1307.6212}, + primaryClass = "astro-ph.IM", + keywords = {methods: data analysis, methods: miscellaneous, virtual observatory tools}, + year = 2013, + month = oct, + volume = 558, + eid = {A33}, + pages = {A33}, + doi = {10.1051/0004-6361/201322068}, + adsurl = {http://adsabs.harvard.edu/abs/2013A%26A...558A..33A}, + adsnote = {Provided by the SAO/NASA Astrophysics Data System} +} diff --git a/paper/paper.md b/paper/paper.md new file mode 100644 index 0000000..4b16db0 --- /dev/null +++ b/paper/paper.md @@ -0,0 +1,120 @@ +--- +title: 'mesa-frames: an extension of mesa for performance and scalability' +tags: + - Python + - Mesa + - Agent-Based Modeling + - Simulation + - Visualization +authors: + - name: Author With ORCID + orcid: 0000-0000-0000-0000 + equal-contrib: true + affiliation: "1, 2" # (Multiple affiliations must be quoted) + - name: Author Without ORCID + equal-contrib: true # (This is how you can denote equal contributions between multiple authors) + affiliation: 2 + - name: Author with no affiliation + corresponding: true # (This is how to denote the corresponding author) + affiliation: 3 + - given-names: LudwigAuthor with affiliation + dropping-particle: van + surname: Surname + affiliation: 3 +affiliations: + - name: Affiliation 1 + index: 1 + ror: 00hx57361 + - name: Institution Name, Country + index: 2 + - name: Independent Researcher, Country + index: 3 +date: 13 August 2017 +bibliography: paper.bib + +# Optional fields if submitting to a AAS journal too, see this blog post: +# https://blog.joss.theoj.org/2018/12/a-new-collaboration-with-aas-publishing +aas-doi: 10.3847/xxxxx <- update this with the DOI from AAS once you know it. +aas-journal: Astrophysical Journal <- The name of the AAS journal. +--- + +# Summary + +The forces on stars, galaxies, and dark matter under external gravitational +fields lead to the dynamical evolution of structures in the universe. The orbits +of these bodies are therefore key to understanding the formation, history, and +future state of galaxies. The field of "galactic dynamics," which aims to model +the gravitating components of galaxies to study their structure and evolution, +is now well-established, commonly taught, and frequently used in astronomy. +Aside from toy problems and demonstrations, the majority of problems require +efficient numerical tools, many of which require the same base code (e.g., for +performing numerical orbit integration). + +# Statement of need + +`Gala` is an Astropy-affiliated Python package for galactic dynamics. Python +enables wrapping low-level languages (e.g., C) for speed without losing +flexibility or ease-of-use in the user-interface. The API for `Gala` was +designed to provide a class-based and user-friendly interface to fast (C or +Cython-optimized) implementations of common operations such as gravitational +potential and force evaluation, orbit integration, dynamical transformations, +and chaos indicators for nonlinear dynamics. `Gala` also relies heavily on and +interfaces well with the implementations of physical units and astronomical +coordinate systems in the `Astropy` package [@astropy] (`astropy.units` and +`astropy.coordinates`). + +`Gala` was designed to be used by both astronomical researchers and by +students in courses on gravitational dynamics or astronomy. It has already been +used in a number of scientific publications [@Pearson:2017] and has also been +used in graduate courses on Galactic dynamics to, e.g., provide interactive +visualizations of textbook material [@Binney:2008]. The combination of speed, +design, and support for Astropy functionality in `Gala` will enable exciting +scientific explorations of forthcoming data releases from the *Gaia* mission +[@gaia] by students and experts alike. + +# Mathematics + +Single dollars ($) are required for inline mathematics e.g. $f(x) = e^{\pi/x}$ + +Double dollars make self-standing equations: + +$$\Theta(x) = \left\{\begin{array}{l} +0\textrm{ if } x < 0\cr +1\textrm{ else} +\end{array}\right.$$ + +You can also use plain \LaTeX for equations +\begin{equation}\label{eq:fourier} +\hat f(\omega) = \int_{-\infty}^{\infty} f(x) e^{i\omega x} dx +\end{equation} +and refer to \autoref{eq:fourier} from text. + +# Citations + +Citations to entries in paper.bib should be in +[rMarkdown](http://rmarkdown.rstudio.com/authoring_bibliographies_and_citations.html) +format. + +If you want to cite a software repository URL (e.g. something on GitHub without a preferred +citation) then you can do it with the example BibTeX entry below for @fidgit. + +For a quick reference, the following citation commands can be used: +- `@author:2001` -> "Author et al. (2001)" +- `[@author:2001]` -> "(Author et al., 2001)" +- `[@author1:2001; @author2:2001]` -> "(Author1 et al., 2001; Author2 et al., 2002)" + +# Figures + +Figures can be included like this: +![Caption for example figure.\label{fig:example}](figure.png) +and referenced from text using \autoref{fig:example}. + +Figure sizes can be customized by adding an optional second parameter: +![Caption for example figure.](figure.png){ width=20% } + +# Acknowledgements + +We acknowledge contributions from Brigitta Sipocz, Syrtis Major, and Semyeong +Oh, and support from Kathryn Johnston during the genesis of this project. + +# References \ No newline at end of file