From 4cce02b113bd4a5ab36c8bd9559c7a157433909d Mon Sep 17 00:00:00 2001 From: The Open Journals editorial robot <89919391+editorialbot@users.noreply.github.com> Date: Fri, 9 Aug 2024 18:22:02 +0100 Subject: [PATCH] Creating 10.21105.joss.06857.jats --- .../paper.jats/10.21105.joss.06857.jats | 966 ++++++++++++++++++ 1 file changed, 966 insertions(+) create mode 100644 joss.06857/paper.jats/10.21105.joss.06857.jats diff --git a/joss.06857/paper.jats/10.21105.joss.06857.jats b/joss.06857/paper.jats/10.21105.joss.06857.jats new file mode 100644 index 0000000000..02e1e77f05 --- /dev/null +++ b/joss.06857/paper.jats/10.21105.joss.06857.jats @@ -0,0 +1,966 @@ + + +
+ + + + +Journal of Open Source Software +JOSS + +2475-9066 + +Open Journals + + + +6857 +10.21105/joss.06857 + +regional-mom6: A Python package for automatic generation +of regional configurations for the Modular Ocean Model 6 + + + +https://orcid.org/0000-0003-3165-8676 + +Barnes +Ashley J. + + + + + +https://orcid.org/0000-0002-8149-4094 + +Constantinou +Navid C. + + + + + + + +https://orcid.org/0000-0001-7577-3604 + +Gibson +Angus H. + + + + +https://orcid.org/0000-0001-8960-9557 + +Kiss +Andrew E. + + + + + +https://orcid.org/0000-0002-6030-1951 + +Chapman +Chris + + + + +https://orcid.org/0000-0003-4001-0230 + +Reilly +John + + + + +https://orcid.org/0000-0002-1222-375X + +Bhagtani +Dhruv + + + + + +https://orcid.org/0000-0001-8570-7424 + +Yang +Luwei + + + + + + +Australian National University, Australia + + + + +ARC Centre of Excellence for Climate Extremes, +Australia + + + + +University of Melbourne, Australia + + + + +ARC Centre of Excellence for the Weather of the 21st +Century, Australia + + + + +CSIRO Environment, Hobart, Tasmania, +Australia + + + + +University of Tasmania, Australia + + + + +8 +8 +2024 + +9 +100 +6857 + +Authors of papers retain copyright and release the +work under a Creative Commons Attribution 4.0 International License (CC +BY 4.0) +2022 +The article authors + +Authors of papers retain copyright and release the work under +a Creative Commons Attribution 4.0 International License (CC BY +4.0) + + + +Python +ocean modeling +regional modeling +mom6 + + + + + + Summary +

regional-mom6 is a Python package that + provides an easy and versatile way to set up regional configurations + of the Modular Ocean Model version 6 (MOM6).

+ + Regional ocean modeling +

In the ocean, fast and small-scale motions (from ~100m to ~100km + varying at time scales of hours to days) play an important role in + shaping the large-scale ocean circulation and climate (length scales + ~10,000km varying at decadal time scales) + (de + Lavergne et al., 2022; + Gula + et al., 2022; + Melet + et al., 2022). Despite the increase in computational power + and the use of graphical processing units that can bring + breakthrough performance and speedup + (Silvestri + et al., 2024), there are always processes, boundary, or + forcing features that are smaller than the model’s grid spacing and, + thus, remain unresolved in global ocean models. Regional ocean + models can be run at higher resolutions while limiting the required + computational resources.

+

A regional ocean model simulates the ocean only in a prescribed + region, which is a subset of the global ocean. To do that, we need + to apply open boundary conditions at the region’s boundaries, that + is, we need to impose conditions that mimic the oceanic flow that we + are not simulating + (Orlanski, + 1976). For example, + [fig:tasman] + shows the surface currents from a regional ocean simulation of the + Tasman sea that was configured using the + regional-mom6 package. The boundaries of the + domain depicted in + [fig:tasman] + are forced with the ocean flow from a global ocean reanalysis + product. Higher-resolution regional ocean models improve the + representation of smaller-scale motions, such as tidal beams, + mixing, mesoscale and sub-mesoscale circulation, as well as the + oceanic response to smaller-scale bathymetric or coastal features + (such as headlands, islands, sea-mounts, or submarine canyons) and + surface forcing (such as atmospheric fronts and convective storms). + Regional modelling further allows for the “downscaling” of + coarse-resolution global ocean or climate models, permitting the + representation of the variation in local conditions that might + otherwise be contained within only a few (or even a single!) model + grid cells in a global model.

+ + + Modular Ocean Model version 6 +

MOM6 is a widely-used open-source, general circulation ocean–sea + ice model, written in Fortran + (Adcroft + et al., 2019). MOM6 contains several improvements over its + predecessor MOM5 + (Griffies, + 2014), including the implementation of the + Arbitrary-Lagrangian-Eulerian vertical coordinates + (Bleck, + 2002; + Griffies + et al., 2020), more efficient tracer advection schemes, and + state-of-the art parameterizations of sub-grid scale physics. + Pertinent for our discussion, MOM6 provides support for open + boundary conditions and thus is becoming popular for regional ocean + modeling studies (see, e.g., Ross et al. + (2023), + Ross et al. + (2024)) + in addition to global configurations. However, setting up a regional + configuration for MOM6 can be challenging, time consuming, and often + involves using several programming languages, a few different tools, + and also manually editing/tweaking some input files. The + regional-mom6 package overcomes these + difficulties, automatically generating a regional MOM6 configuration + of the user’s choice with relatively simple domain geometry, that + is, rectangular domains.

+ +

Snapshot of the ocean surface speed from a two-tier, + one-way nested regional ocean configurations of the East + Australian Current. The outer regional configuration (dashed + region) uses 1/10ᵒ horizontal resolution, 75 vertical levels, and + is forced by the output from the global ocean–sea ice model at + 1/10ᵒ horizontal resolution (ACCESS-OM2-01; Kiss et al. + (2020)). + The inner regional configuration (dotted region) uses 1/30ᵒ + horizontal resolution, 100 vertical levels, and is forced with the + outer regional model. All simulations share a common inter-annual + atmospheric forcing from 1990 to 2018 provided by the JRA55-do + reanalysis + (Tsujino + et al., + 2018).

+ + + + + <monospace>regional-mom6</monospace> +

The regional-mom6 package takes as input + various datasets that contain the ocean initial condition, the + boundary forcing (ocean and atmosphere) for the regional domain, and + the seafloor topography. The input datasets can be on the Arakawa A, + B, or C grids + (Arakawa + & Lamb, 1977); the package performs the appropriate + interpolation using xESMF + (Zhuang + et al., 2023) under the hood, to put the everything on the C + grid required by MOM6. This base grid for the regional configuration + can be constructed in two ways, either by the user defining a + desired resolution and choosing between pre-configured options, or + by the user providing pre-existing horizontal and/or vertical MOM6 + grids. The user can use MOM6’s Arbitrary-Lagrangian-Eulerian + vertical coordinates, regardless of the native vertical coordinates + of the boundary forcing input. The package automates the re-gridding + of all the required forcing input, takes care of all the metadata + encoding, generates the regional grid, and ensures that the final + input files are in the format expected by MOM6. Additionally, the + tricky case of a regional configuration that includes the ‘seam’ in + the longitude of the raw input data (e.g., a 10ᵒ-wide regional + configuration centred at Fiji (178ᵒE) and forced by input with + native longitude coordinate in the range 180ᵒW–180ᵒE) is handled + automatically, removing the need for any preprocessing of the input + data. This automation allows users to set up a regional MOM6 + configuration using only Python and from the convenience of a single + Jupyter notebook. Herzfeld et al. + (2011) + provide rules of thumb to guide the user in setting regional grid + parameters such as the resolution.

+

regional-mom6 is installable via + conda, it is continuously tested, and comes + with extensive documentation including tutorials and examples for + setting up regional MOM6 configurations using publicly-available + forcing and bathymetry datasets (namely, the GLORYS dataset for + ocean boundary forcing + (Copernicus + Marine Services, 2024), the ERA5 reanalysis for atmospheric + forcing + (Copernicus + Climate Change Service, 2024), and the GEBCO dataset for + seafloor topography + (GEBCO + Bathymetric Compilation Group 2023, 2023)).

+

With the entire process for setting up a regional configuration + streamlined to run within a Jupyter notebook, the package + dramatically reduces the barrier-to-entry for first-time users, or + those without a strong background in Fortran, experience in + compiling and running scripts in terminals, and manipulating netCDF + files. Besides making regional modelling with MOM6 more accessible, + our package can automate the generation of multiple experiments + (e.g., a series of perturbation experiments), saving time and + effort, and improving reproducibility.

+

We designed regional-mom6 with automation + of regional configurations in mind. However, the package’s code + design and modularity make more complex configurations possible + since users can use their own custom-made grids with more complex + boundaries and construct the boundary forcing terms one by one.

+ + + + Statement of need +

The learning curve for setting up a regional ocean model can be + steep, and it is not obvious for a new user what inputs are required, + nor the appropriate format. In the case of MOM6, there are several + tools scattered in Github repositories, for example those collected in + Earth System Modeling Group grid tools + (Simkins + et al., 2021). Also, there exist several regional configuration + examples but they are hardcoded for particular domains, specific input + files, and work only on specific high-performance computing machines + (e.g., Ross et al. + (2023)).

+

Until now there has been no one-stop-shop for users to learn how to + get a regional MOM6 configuration up and running. Users are required + to use several tools in several programming languages and then modify + – sometimes by hand – some of the input metadata to bring everything + into the format that MOM6 expects. Many parts of this process are not + documented, requiring users to dig into the MOM6 Fortran source code. + Recently, the Climate, Ecosystems and Fisheries Initiative gathered + some tools into a single repository + (Teng + et al., 2023) but, at the moment, they are written for specific + inputs and computational environment and not installable as a Python + package. Other ocean models have packages to aid in regional + configuration setup, for example Pyroms + (Hedstrom + & contributors, 2023) for the Regional Oceanic Modelling + System (ROMS; Shchepetkin & McWilliams + (2005)) + and MITgcm_python + (Naughten + & Jones, 2023) for the Massachusetts Institute of + Technology General Circulation Model (MITgcm; Marshall et al. + (1997)). + With MOM6’s growing user base for regional applications, there is a + need for a platform that walks users through regional domain + configuration from start to finish and, ideally, automates the process + on the way. Other than reducing the barrier-to-entry, automating the + regional configuration process renders the workflow much more + reproducible; see discussion by Polton et al. + (2023). + regional-mom6 precisely meets these needs.

+

By having a shared set of tools that the community can work with + and contribute to, this package also facilitates collaboration and + knowledge-sharing between different research groups. Using a shared + framework for setting up regional models, it is easier to compare and + contrast examples of different experiments and allows for users to + gain intuition for generating their chosen domain.

+

regional-mom6 package can also be used for + educational purposes, for example as part of course curricula. With + the technically-challenging aspects of setting up a regional + configuration now being automated by the + regional-mom6 package, students can set up and + run simple MOM6 regional configurations and also change parameters + like the model’s resolution or the forcing, run again, and see how + these parameters affect the ocean flow.

+ + + Acknowledgements +

We thank the vibrant community of the Consortium for Ocean–Sea Ice + Modeling in Australia + (cosima.org.au) + and also Josué Martínez-Moreno and Callum Shakespeare for useful + discussions during the development of this package. We acknowledge + support from the Australian Research Council under DECRA Fellowship + DE210100749 (N.C.C.), grant LP200100406 (A.E.K.), and the Center of + Excellences for Climate Extremes CE170100023 and for the Weather of + the 21st Century CE230100012. We would also like to acknowledge the + code and notes by James Simkins, Andrew Ross, and Rob Cermak, which + helped us to troubleshoot and improve the algorithms in our package. + Last, we thank the three reviewers and the editor for their efforts + and remarks.

+ + + + + + + + + AdcroftAlistair + AndersonWhit + BalajiV. + BlantonChris + BushukMitchell + DufourCarolina O. + DunneJohn P. + GriffiesStephen M. + HallbergRobert + HarrisonMatthew J. + HeldIsaac M. + JansenMalte F. + JohnJasmin G. + KrastingJohn P. + LangenhorstAmy R. + LeggSonya + LiangZhi + McHughColleen + RadhakrishnanAparna + ReichlBrandon G. + RosatiTony + SamuelsBonita L. + ShaoAndrew + StoufferRonald + WintonMichael + WittenbergAndrew T. + XiangBaoqiang + ZadehNiki + ZhangRong + + The GFDL global ocean and sea ice model OM4.0: Model description and simulation features + Journal of Advances in Modeling Earth Systems + 2019 + 11 + 10 + 10.1029/2019MS001726 + 3167 + 3211 + + + + + + MarshallJohn + AdcroftAlistair + HillChris + PerelmanLev + HeiseyCurt + + A finite-volume, incompressible Navier Stokes model for studies of the ocean on parallel computers + Journal of Geophysical Research: Oceans + 1997 + 102 + C3 + 10.1029/96JC02775 + 5753 + 5766 + + + + + + ShchepetkinAlexander F + McWilliamsJames C + + The regional oceanic modeling system (ROMS): A split-explicit, free-surface, topography-following-coordinate oceanic model + Ocean Modelling + 2005 + 9 + 4 + 10.1016/j.ocemod.2004.08.002 + 347 + 404 + + + + + + ZhuangJiawei + DussinRaphael + HuardDavid + BourgaultPascal + BanihirweAnderson + RaynaudStephane + MalevichBrewster + SchupfnerMartin + Filipe + LevangSam + GauthierCharles + JülingAndré + AlmansiMattia + ScottRichard + RondeauG + RaspStephan + SmithTrevor James + StachelekJemma + PloughMatthew + LiXianxiang + + xESMF: Universal regridder for geospatial data + GitHub repository + Zenodo + 2023 + https://github.com/pangeo-data/xESMF + 10.5281/zenodo.4294774 + + + + + + NaughtenKaitlin + JonesDani + + MITgcm_python + GitHub repository + GitHub + 2023 + https://github.com/knaughten/mitgcm_python + + + + + + HedstromKate + contributors + + Pyroms + GitHub repository + GitHub + 2023 + https://github.com/ESMG/pyroms + + + + + + SimkinsJames + CermakRob + HedstromKate + GibsonAngus + + Earth System Modeling Group (ESMG) gridtools + GitHub repository + GitHub + 2021 + https://github.com/ESMG/gridtools + + + + + + GEBCO Bathymetric Compilation Group 2023 + + The GEBCO_2023 Grid - a continuous terrain model of the global oceans and land + NERC EDS British Oceanographic Data Centre NOC + 2023 + https://doi.org/10.5285/f98b053b-0cbc-6c23-e053-6c86abc0af7b + 10.5285/f98b053b-0cbc-6c23-e053-6c86abc0af7b + + + + + + Copernicus Marine Services + + Global ocean physics reanalysis + Mercator Ocean International + 2024 + https://doi.org/10.48670/moi-00021 + 10.48670/moi-00021 + + + + + + PoltonJ. + HarleJ. + HoltJ. + KatavoutaA. + PartridgeD. + JardineJ. + WakelinS. + RulentJ. + WiseA. + HutchinsonK. + ByrneD. + BruciaferriD. + O’DeaE. + De DominicisM. + MathiotP. + CowardA. + YoolA. + PalmiériJ. + LessinG. + Mayorga-AdameC. G. + Le GuennecV. + ArnoldA. + RoussetC. + + Reproducible and relocatable regional ocean modelling: Fundamentals and practices + Geoscientific Model Development + 2023 + 16 + 5 + 10.5194/gmd-16-1481-2023 + 1481 + 1510 + + + + + + Copernicus Climate Change Service + + ECMWF Reanalysis v5 + European Centre for Medium-Range Weather Forecasts + 2024 + https://doi.org/10.48670/moi-00021 + 10.48670/moi-00021 + + + + + + RossA. C. + StockC. A. + KoulV. + DelworthT. L. + LuF. + WittenbergA. + AlexanderM. A. + + Dynamically downscaled seasonal ocean forecasts for North American East Coast ecosystems + EGUsphere + 2024 + 2024 + https://egusphere.copernicus.org/preprints/2024/egusphere-2024-394/ + 10.5194/egusphere-2024-394 + 1 + 40 + + + + + + RossA. C. + StockC. A. + AdcroftA. + CurchitserE. + HallbergR. + HarrisonM. J. + HedstromK. + ZadehN. + AlexanderM. + ChenW. + DrenkardE. J. + PontaviceH. du + DussinR. + GomezF. + JohnJ. G. + KangD. + LavoieD. + ResplandyL. + RoobaertA. + SabaV. + ShinS.-I. + SiedleckiS. + SimkinsJ. + + A high-resolution physical–biogeochemical model for marine resource applications in the northwest Atlantic (MOM6-COBALT-NWA12 v1.0) + Geoscientific Model Development + 2023 + 16 + 23 + https://gmd.copernicus.org/articles/16/6943/2023/ + 10.5194/gmd-16-6943-2023 + 6943 + 6985 + + + + + + ArakawaA. + LambV. R. + + Computational design of the basic dynamical processes of the UCLA general circulation model + Methods in Computational Physics: Advances in Research and Applications + 1977 + 17 + Supplement C + 10.1016/B978-0-12-460817-7.50009-4 + 173 + 265 + + + + + + GriffiesS. M. + + Elements of the modular ocean model (MOM) + GFDL Ocean Group Tech. Rep. + 2014 + 7 + https://mom-ocean.github.io/assets/pdfs/MOM5_manual.pdf + 47 + + + + + + + HerzfeldM. + SchmidtM. + GriffiesS. M. + LiangZ. + + Realistic test cases for limited area ocean modelling + Ocean Modelling + 2011 + 37 + 1 + 10.1016/j.ocemod.2010.12.008 + 1 + 34 + + + + + + GriffiesS. M. + AdcroftA. + HallbergR. W. + + A primer on the vertical Lagrangian-remap method in ocean models based on finite volume generalized vertical coordinates + Journal of Advances in Modeling Earth Systems + 2020 + 12 + 10 + 10.1029/2019MS001954 + e2019MS001954 + + + + + + + GulaJonathan + TaylorJohn + ShcherbinaAndrey + MahadevanAmala + + Chapter 8 – submesoscale processes and mixing + Ocean mixing + + MeredithMichael + Naveira GarabatoAlberto + + Elsevier + 2022 + 978-0-12-821512-8 + 10.1016/B978-0-12-821512-8.00015-3 + 181 + 214 + + + + + + de LavergneCasimir + GroeskampSjoerd + ZikaJan + JohnsonHelen L. + + Chapter 3 – the role of mixing in the large-scale ocean circulation + Ocean mixing + + MeredithMichael + Naveira GarabatoAlberto + + Elsevier + 2022 + 978-0-12-821512-8 + 10.1016/B978-0-12-821512-8.00010-4 + 35 + 63 + + + + + + MeletAngélique V. + HallbergRobert + MarshallDavid P. + + Chapter 2 – the role of ocean mixing in the climate system + Ocean mixing + + MeredithMichael + Naveira GarabatoAlberto + + Elsevier + 2022 + 978-0-12-821512-8 + 10.1016/B978-0-12-821512-8.00009-8 + 5 + 34 + + + + + + OrlanskiI. + + A simple boundary condition for unbounded hyperbolic flows + Journal of Computational Physics + 1976 + 21 + 3 + 10.1016/0021-9991(76)90023-1 + 251 + 269 + + + + + + BleckRainer + + An oceanic general circulation model framed in hybrid isopycnic-Cartesian coordinates + Ocean Modelling + 2002 + 4 + 1 + 10.1016/S1463-5003(01)00012-9 + 55 + 88 + + + + + + TengYi-Cheng + RossAndrew + MorrisonTheresa + + CEFI-regional-MOM6: Essential tools, XML files, and source codes for collaborators of the Climate, Ecosystems, and Fisheries Initiative (CEFI) to conduct simulations + GitHub repository + GitHub + 2023 + https://github.com/NOAA-GFDL/CEFI-regional-MOM6 + + + + + + KissA. E. + HoggA. McC. + HannahN. + Boeira DiasF. + BrassingtonG. B. + ChamberlainM. A. + ChapmanC. + DobrohotoffP. + DominguesC. M. + DuranE. R. + EnglandM. H. + FiedlerR. + GriffiesS. M. + HeerdegenA. + HeilP. + HolmesR. M. + KlockerA. + MarslandS. J. + MorrisonA. K. + MunroeJ. + NikurashinM. + OkeP. R. + PiloG. S. + RichetO. + SavitaA. + SpenceP. + StewartK. D. + WardM. L. + WuF. + ZhangX. + + ACCESS-OM2 v1.0: A global ocean–sea ice model at three resolutions + Geoscientific Model Development + 2020 + 13 + 2 + 10.5194/gmd-13-401-2020 + 401 + 442 + + + + + + TsujinoHiroyuki + UrakawaShogo + NakanoHideyuki + SmallR. Justin + KimWho M. + YeagerStephen G. + DanabasogluGokhan + SuzukiTatsuo + BamberJonathan L. + BentsenMats + BöningClaus W. + BozecAlexandra + ChassignetEric P. + CurchitserEnrique + Boeira DiasFabio + DurackPaul J. + GriffiesStephen M. + HaradaYayoi + IlicakMehmet + JoseySimon A. + KobayashiChiaki + KobayashiShinya + KomuroYoshiki + LargeWilliam G. + Le SommerJulien + MarslandSimon J. + MasinaSimona + ScheinertMarkus + TomitaHiroyuki + ValdiviesoMaria + YamazakiDai + + JRA-55 based surface dataset for driving ocean–sea-ice models (JRA55-do) + Ocean Modelling + 2018 + 130 + 10.1016/j.ocemod.2018.07.002 + 79 + 139 + + + + + + SilvestriSimone + WagnerGregory L. + ConstantinouNavid C + HillChristopher + CampinJean-Michel + SouzaAndre Nogueira + BishnuSiddhartha + ChuravyValentin + MarshallJohn C + FerrariRaffaele + + A GPU-based ocean dynamical core for routine mesoscale-resolving climate simulations + ESS Open Archive + 2024 + 10.22541/essoar.171708158.82342448/v1 + + + + +