doc: JOSS template

.github/workflows/draft-pdf.yml

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+on:
+  push:
+    branches:
+      - main
+      - paper.md
+      - paper.md-*
+  pull_request:
+    branches:
+      - main
+      - paper.md
+
+jobs:
+  paper:
+    runs-on: ubuntu-latest
+    name: Paper Draft
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+      - name: Build draft PDF
+        uses: openjournals/[email protected]
+        with:
+          journal: joss
+          # This should be the path to the paper within your repo.
+          paper-path: joss/paper.md
+      - name: Upload
+        uses: actions/upload-artifact@v1
+        with:
+          name: paper
+          # This is the output path where Pandoc will write the compiled
+          # PDF. Note, this should be the same directory as the input
+          # paper.md
+          path: joss/paper.pdf

joss/paper.bib

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+@Article{Edwards:2018ccc,
+  author        = {Edwards, Faber and Kendall, Emily and Hotchkiss, Shaun and Easther, Richard},
+  journal       = {JCAP},
+  title         = {PyUltraLight: A Pseudo-Spectral Solver for Ultralight Dark Matter Dynamics},
+  year          = {2018},
+  pages         = {027},
+  volume        = {10},
+  archiveprefix = {arXiv},
+  doi           = {10.1088/1475-7516/2018/10/027},
+  eprint        = {1807.04037},
+  primaryclass  = {astro-ph.CO},
+}
+
+@Article{Glennon:2022huu,
+  author        = {Glennon, Noah and Nadler, Ethan O. and Musoke, Nathan and Banerjee, Arka and Prescod-Weinstein, Chanda and Wechsler, Risa H.},
+  journal       = {Physical Review D},
+  title         = {Tidal disruption of solitons in self-interacting ultralight axion dark matter},
+  year          = {2022},
+  month         = {5},
+  number        = {12},
+  pages         = {123540},
+  volume        = {105},
+  abstract      = {Ultralight axions (ULAs) are promising dark matter candidates that can have a distinct impact on the formation and evolution of structure on nonlinear scales relative to the cold, collisionless dark matter (CDM) paradigm. However, most studies of structure formation in ULA models do not include the effects of self-interactions, which are expected to arise generically. Here, we study how the tidal evolution of solitons is affected by ULA self-interaction strength and sign. Specifically, using the pseudospectral solver UltraDark.jl, we simulate the tidal disruption of self-interacting solitonic cores as they orbit a $10^{11}~M_{\mathrm{\odot}}$ Navarro-Frenk-White CDM host halo potential for a range of orbital parameters, assuming a fiducial ULA particle mass of $10^{-22}\mathrm{eV}$. We find that repulsive (attractive) self-interactions significantly accelerate (decelerate) soliton tidal disruption. We also identify a degeneracy between the self-interaction strength and soliton mass that determines the efficiency of tidal disruption, such that disruption timescales are affected at the $\sim 50\%$ level for variations in the dimensionless ULA self-coupling from $\lambda=-10^{-92}$ to $\lambda=10^{-92}$.},
+  archiveprefix = {arXiv},
+  copyright     = {Creative Commons Attribution Non Commercial No Derivatives 4.0 International},
+  date          = {2022-05-20},
+  doi           = {10.1103/physrevd.105.123540},
+  eprint        = {2205.10336},
+  keywords      = {Cosmology and Nongalactic Astrophysics (astro-ph.CO), High Energy Physics - Phenomenology (hep-ph), FOS: Physical sciences},
+  primaryclass  = {astro-ph.CO},
+  publisher     = {American Physical Society ({APS})},
+}
+
+@Article{Glennon:2023jsp,
+  author        = {Glennon, Noah and Musoke, Nathan and Prescod-Weinstein, Chanda},
+  journal       = {Physical Review D},
+  title         = {Simulations of multi-field ultralight axion-like dark matter},
+  year          = {2023},
+  month         = {2},
+  number        = {6},
+  pages         = {063520},
+  volume        = {107},
+  abstract      = {As constraints on ultralight axion-like particles (ALPs) tighten, models with multiple species of ultralight ALP are of increasing interest. We perform simulations of two-ALP models with particles in the currently supported range [arXiv:1307.1705] of plausible masses. The code we modified, UltraDark.jl, not only allows for multiple species of ultralight ALP with different masses, but also different self-interactions and inter-field interactions. This allows us to perform the first three-dimensional simulations of two-field ALPs with self-interactions and inter-field interactions. Our simulations show that having multiple species and interactions introduces different phenomenological effects as compared to a single field, non-interacting scenarios. In particular, we explore the dynamics of solitons. Interacting multi-species ultralight dark matter has different equilibrium density profiles as compared to single-species and/or non-interacting ultralight ALPs. As seen in earlier work [arXiv:2011.09510], attractive interactions tend to contract the density profile while repulsive interactions spread out the density profile. We also explore collisions between solitons comprised of distinct axion species. We observe a lack of interference patterns in such collisions, and that resulting densities depend on the relative masses of the ALPs and their interactions.},
+  archiveprefix = {arXiv},
+  copyright     = {Creative Commons Attribution Non Commercial No Derivatives 4.0 International},
+  date          = {2023-02-08},
+  doi           = {10.1103/physrevd.107.063520},
+  eprint        = {2302.04302},
+  keywords      = {Cosmology and Nongalactic Astrophysics (astro-ph.CO), High Energy Physics - Phenomenology (hep-ph), FOS: Physical sciences},
+  primaryclass  = {astro-ph.CO},
+  publisher     = {American Physical Society ({APS})},
+}
+
+@Article{Glennon:2023oqa,
+  author        = {Glennon, Noah and Mirasola, Anthony E. and Musoke, Nathan and Neyrinck, Mark C. and Prescod-Weinstein, Chanda},
+  title         = {Scalar dark matter vortex stabilization with black holes},
+  year          = {2023},
+  month         = {1},
+  abstract      = {Galaxies and their dark-matter halos are commonly presupposed to spin. But it is an open question how this spin manifests in halos and soliton cores made of scalar dark matter (SDM, including fuzzy/wave/ultralight-axion dark matter). One way spin could manifest in a necessarily irrotational SDM velocity field is with a vortex. But recent results have cast doubt on this scenario, finding that vortices are generally unstable except with substantial repulsive self-interaction. In this paper, we introduce an alternative route to stability: in both (non-relativistic) analytic calculations and simulations, a black hole or other central mass at least as massive as a soliton can stabilize a vortex within it. This conclusion may also apply to stellar-scale Bose stars.},
+  archiveprefix = {arXiv},
+  copyright     = {Creative Commons Attribution Non Commercial No Derivatives 4.0 International},
+  doi           = {10.48550/ARXIV.2301.13220},
+  eprint        = {2301.13220},
+  keywords      = {Cosmology and Nongalactic Astrophysics (astro-ph.CO), Astrophysics of Galaxies (astro-ph.GA), High Energy Physics - Phenomenology (hep-ph), FOS: Physical sciences},
+  primaryclass  = {astro-ph.CO},
+  publisher     = {arXiv},
+}

joss/paper.md

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+---
+title: 'UltraDark.jl: A Julia package for simulation of cosmological scalar fields'
+tags:
+  - Julia
+  - cosmology
+  - dark matter
+  - inflation
+  - scalar field
+  - dynamics
+authors:
+  - name: Nathan Musoke
+    orcid:  0000-0001-9839-9256
+    affiliation: "1" # (Multiple affiliations must be quoted)
+affiliations:
+ - name: Department of Physics & Astronomy, University of New Hampshire, USA
+   index: 1
+date: 1 June 2023
+bibliography: paper.bib
+
+---
+
+# Summary
+
+
+# Statement of need
+
+
+# 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:
+
+- @Glennon:2023oqa  ->  "Author et al. (2001)"
+- [@Glennon:2023jsp] -> "(Author et al., 2001)"
+- [Edwards:2018ccc; @Glennon:2022huu] -> "(Author1 et al., 2001; Author2 et al., 2002)"
+
+# Figures
+
+Figures can be included like this:
+![Caption for example figure.\label{fig:example}](../benchmarks/time_step/cpus.pdf)
+and referenced from text using \autoref{fig:example}.
+
+Figure sizes can be customized by adding an optional second parameter:
+![Caption for example figure.](../benchmarks/time_step/resol.pdf){ width=20% }
+
+# Acknowledgements
+
+
+# References