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Edits for JOSS submission #7

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33 changes: 21 additions & 12 deletions paper/paper.bib
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,8 @@ @article{Marshall:1997
number={C3},
pages={5733--5752},
year={1997},
publisher={Wiley Online Library}
publisher={Wiley Online Library},
doi={10.1029/96jc02776}
}

@article{Bell:2018,
Expand Down Expand Up @@ -37,7 +38,7 @@ @article{Hack:1992
}

@book{Langton:2008,
title={Atmospheric dynamics on strongly irradiated Jovian planets},
title={Atmospheric dynamics on strongly irradiated {Jovian} planets},
author={Langton, Jonathan},
year={2008},
publisher={University of California, Santa Cruz}
Expand All @@ -52,7 +53,8 @@ @article{Feng:2016
number={1},
pages={52},
year={2016},
publisher={IOP Publishing}
publisher={IOP Publishing},
doi={10.3847/0004-637x/829/1/52}
}

@ARTICLE{Menou:2009,
Expand Down Expand Up @@ -156,7 +158,8 @@ @article{Way:2017
number={1},
pages={12},
year={2017},
publisher={IOP Publishing}
publisher={IOP Publishing},
doi={10.3847/1538-4365/aa7a06}
}


Expand All @@ -168,7 +171,8 @@ @article{Ferrari:2011
number={3-4},
pages={171--186},
year={2011},
publisher={Elsevier}
publisher={Elsevier},
doi={10.1016/j.ocemod.2011.02.013}
}

@ARTICLE{Brueshaber:2019,
Expand Down Expand Up @@ -224,14 +228,15 @@ @ARTICLE{Showman:2011
}

@article{Langton:2008b,
title={Hydrodynamic simulations of unevenly irradiated Jovian planets},
title={Hydrodynamic simulations of unevenly irradiated {Jovian} planets},
author={Langton, Jonathan and Laughlin, Gregory},
journal={The Astrophysical Journal},
volume={674},
number={2},
pages={1106},
year={2008},
publisher={IOP Publishing}
publisher={IOP Publishing},
doi={10.1086/523957}
}
@ARTICLE{Perez-Becker:2013,
author = {{Perez-Becker}, Daniel and {Showman}, Adam P.},
Expand Down Expand Up @@ -260,7 +265,8 @@ @article{Harris:2020
number={7825},
pages={357--362},
year={2020},
publisher={Nature Publishing Group}
publisher={Nature Publishing Group},
doi={10.1038/s41586-020-2649-2}
}

@ARTICLE{Hunter:2007,
Expand All @@ -274,14 +280,15 @@ @ARTICLE{Hunter:2007
doi={10.1109/MCSE.2007.55}}

@article{Virtanen:2020,
title={SciPy 1.0: fundamental algorithms for scientific computing in Python},
title={SciPy 1.0: fundamental algorithms for scientific computing in {Python}},
author={Virtanen, Pauli and Gommers, Ralf and Oliphant, Travis E and Haberland, Matt and Reddy, Tyler and Cournapeau, David and Burovski, Evgeni and Peterson, Pearu and Weckesser, Warren and Bright, Jonathan and others},
journal={Nature methods},
volume={17},
number={3},
pages={261--272},
year={2020},
publisher={Nature Publishing Group}
publisher={Nature Publishing Group},
doi={10.1038/s41592-019-0686-2}
}

@article{Gelb:2001,
Expand All @@ -291,7 +298,8 @@ @article{Gelb:2001
volume={129},
number={9},
pages={2346--2360},
year={2001}
year={2001},
doi={10.1175/1520-0493(2001)129<2346:svfswe>2.0.co;2}
}

@ARTICLE{Burns:2020,
Expand Down Expand Up @@ -321,5 +329,6 @@ @article{Dunne:2020
number={11},
pages={e2019MS002015},
year={2020},
publisher={Wiley Online Library}
publisher={Wiley Online Library},
doi={10.1029/2019ms002015}
}
14 changes: 7 additions & 7 deletions paper/paper.md
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Expand Up @@ -24,18 +24,18 @@ bibliography: paper.bib

# Summary

In order to answer questions about potential habitability of exoplanets, it is important to develop a robust understanding of a variety of dynamic
processes that can take place in exoplanetary atmospheres. While many exoplanets are readily characterized with current facilities like Hubble and James Webb Space Telescope, exoplanet scientists work with indirect and limited observations of the planets that they study. In order to form hypotheses about their climate, weather, and atmospheric composition, astronomers need robust models that demonstrate how atmospheres act under different conditions. One-dimensional energy-balance models can capture complex mechanisms such as cloud formation and can rapidly explore the parameter ranges, but they fail to account for variations with longitude. In contrast, three-dimensional models capture the variation in latitude, longitude, and altitude, but they are computationally expensive, sometimes taking months to explore the parameter regimes. Their complexity can also obscure the mechanisms that govern atmospheric phenomena. This leaves a natural gap for two-dimensional models, which can capture the spatial variability as well as rapidly explore the parameter space and study the dynamical mechanisms.
In order to answer questions about potentially habitability of exoplanets, it is important to develop a robust understanding of a variety of dynamic
processes that can take place in exoplanetary atmospheres. While many exoplanets are readily characterized with current facilities like Hubble and James Webb Space Telescope, exoplanet scientists work with indirect and limited observations of the planets that they study. To form hypotheses about their climate, weather, and atmospheric composition, astronomers need robust models that demonstrate how atmospheres act under different conditions. One-dimensional energy-balance models can capture complex mechanisms such as cloud formation and can rapidly explore the parameter ranges, but they fail to account for variations with longitude. In contrast, three-dimensional models capture the variation in latitude, longitude, and altitude, but they are computationally expensive, sometimes taking months to explore the parameter regimes. Their complexity can also obscure the mechanisms that govern atmospheric phenomena. This leaves a natural gap for two-dimensional models, which can capture the spatial variability as well as rapidly explore the parameter space and study the dynamical mechanisms.

`SWAMPE` is a Python package for modeling the dynamics of exoplanetary atmospheres. `SWAMPE` is an intermediate-complexity, two-dimensional shallow-water general circulation model. Benchmarked for synchronously rotating hot Jupiters and sub-Neptunes,
the code is modular and could be easily modified to model dissimilar space objects, from Brown Dwarfs to terrestrial, potentially habitable exoplanets.


# Modeling Exoplanet Atmospheres with SWAMPE

Exoplanets exist in a vast range of orbital and planetary parameters. `SWAMPE` is designed to be adaptable to a variety of possible regimes. The user can specify physical parameters such as radius, surface gravity, rotation rate, stellar radiation, and scale height.
Exoplanets exist in a vast range of orbital and planetary parameters. `SWAMPE` is designed to be adaptable to a variety of possible regimes. The user can specify physical parameters such as radius, surface gravity, rotation rate, stellar radiation, and scale height.

`SWAMPE` solves the shallow-water equations using the spectral method [@Hack:1992], with a modified Euler's method timestepping scheme [@Langton:2008]. To ensure numerical-stability, two filters are applied: the modal-splitting filter [@Hack:1992] and a sixth-degree hyperviscosity filter [@Gelb:2001]. `SWAMPE` has the capability to save simulation data at any user-specified frequency. The model outputs geopotential maps and the associated wind fields, which can be used to make inferences about the temperature profiles of exoplanet atmospheres and the dynamical mechanisms behind them. Sample `SWAMPE` outputs are illustrated in figure \autoref{fig:SWAMPE-output}.
`SWAMPE` solves the shallow-water equations using the spectral method [@Hack:1992], with a modified Euler's method time-stepping scheme [@Langton:2008]. To ensure numerical stability, two filters are applied: the modal-splitting filter [@Hack:1992] and a sixth-degree hyperviscosity filter [@Gelb:2001]. `SWAMPE` can save simulation data at any user-specified frequency. The model outputs geopotential maps and the associated wind fields, which can be used to make inferences about the temperature profiles of exoplanet atmospheres and the dynamical mechanisms behind them. Sample `SWAMPE` outputs are illustrated in figure \autoref{fig:SWAMPE-output}.

![Sample `SWAMPE` output: geopotential maps for a hot Jupiter exoplanet at three values of radiative timescale $\tau_{\rm rad}$: 0.1 days, 1 day, and 10 days. This is a replication of the results in @Perez-Becker:2013 for a high insolation, no-drag regime. \label{fig:SWAMPE-output}](timescale_example-1.png)

Expand All @@ -47,7 +47,7 @@ energy-balance models can capture complex mechanisms [e.g., @Bell:2018]
and can rapidly explore the parameter space, but they fail to account for longitudinal variation.
Furthermore, recent observations of giant exoplanets have shown that one-dimensional models
cannot completely describe some of the key atmospheric processes [e.g., @Feng:2016].
On the other hand, complex three-dimensional (3D) models are able to capture variation in the physical space.
On the other hand, complex three-dimensional (3D) models can capture variation in the physical space.
They are frequently based on primitive equations [e.g., @Menou:2009; @Kataria:2016;
@Parmentier:2013] or on the Navier-Stokes equations
[e.g., @Cooper:2006; @Dobbs-Dixon:2013] and can be used to understand a variety of radiative,
Expand All @@ -58,12 +58,12 @@ to explore the parameter space.
The difference in capability between 1D and 3D models leaves a natural gap for two-dimensional
shallow-water models, which can capture the spatial variability as well as run fast enough to
rapidly explore the parameter space and study the dynamical mechanisms. In particular, shallow-water models have been used to study solar system planets, including Earth
[e.g., @Ferrari:2011; @Brueshaber:2019]. Outside of the solar system,
[e.g., @Ferrari:2011; @Brueshaber:2019]. Outside the solar system,
shallow-water models have been used to understand a variety of atmospheric phenomena of hot Jupiters,
such as atmospheric variability [@Menou:2003] and superrotation [@Showman:2011].
They have also been used to make observational predictions for hot Jupiters [e.g., @Langton:2008b;
@Perez-Becker:2013]. However, many of these models are written in Fortran, which makes them difficult to adapt
for the varied needs of exoplanetary science.
to the varied needs of exoplanetary science.

`SWAMPE` offers a fully Python, open-source implementation of the 2D shallow-water system. This package does not require multiple cores, and is flexible and modular. `SWAMPE` is designed to be easily modified to model dissimilar space objects, from Brown Dwarfs to terrestrial, potentially habitable exoplanets. `SWAMPE` provides the capability to conduct
wide parameter sweeps and to produce maps of the thermal and wind properties of the planets in latitude and longitude, which can be used to help constrain and make predictions for observations of their atmospheres.
Expand Down