OMesh2KRAKEN

OMesh2KRAKEN: A tool for mesh generation with OceanMesh2D for underwater acoustic modeling with KRAKEN

OMesh2KRAKEN is under development by Nuno Monteiro ([email protected]) and Tiago Oliveira ([email protected]), and it is distributed under the GNU Public License. A detailed description about OMesh2KRAKEN can be found at https://doi.org/10.1016/j.advengsoft.2023.103455.

Current version:
version 1.1 (December 19, 2022): significant changes made in OceanMesh2D/@msh/private/writekraken3d.m, in tests/tagus_estuary/Run_OM2D_*.m, and in tests/azores/Run_OM2D_*.m; minor changes made in utils/calc_ss.m and OceanMesh2D/@msh/msh.m.

Archived (deprecated) versions:
version 1.0 (September 11, 2022)

How to cite this product [APA format]:
Monteiro, N.M.R., & Oliveira, T.C.A. (2023). Mesh generation for underwater acoustic modeling with KRAKEN. Advances in Engineering Software, 180, 103455. https://doi.org/10.1016/j.advengsoft.2023.103455

Dependencies

• MATLAB (R2021a or above)
• OceanMesh2D v4.0
• Acoustics Toolbox (2020_11_4 version)
• m_map package

General description of directories

• atWin10_2020_11_4: Contains the Acoustics Toolbox (Windows version at [1]). The original tests/ folder from the Acoustics Toolbox was removed to save space;
• data: Contains environmental data (temperature and salinity), bathymetry and shoreline datasets to run the two tests;
• m_map: A mapping package for Matlab (dependency for OceanMesh2D) [2];
• OceanMesh2D: OceanMesh2D toolbox [3] adapted to OMesh2Kraken. Specific adaptations were made to OceanMesh2D: the msh.m script in OceanMesh2d/@msh/ was changed, and two function scripts (writekraken3d.m, calc_ss.m) were created in OceanMesh2D/@msh/private. Some unnecessary folders from the original version were removed to save space;
• tests: Tagus Estuary and Azores study cases shown in Sections 3.1 and 3.2 of the paper, respectivelly, to test OMesh2KRAKEN;
• utils: Contains functions for pre/post-processing purposes (e.g., to calculate the sound speed, make bathymetry field plots), where functions brewermap.m and sndspd.m come from [4] and [5], respectively, while remaining (find_nearest_point.m, plot_mesh_bathy.m, calc_ss.m and surf2D_TL.m) are custom made for OMesh2Kraken.

How to use OMesh2KRAKEN

Here we present hands-on instructions to reproduce the Tagus estuary study case results:

1. Go to the tests/tagus_estuary/ folder from the main directory and execute Run_OM2D_Tagus_Estuary.m;
2. In the same directory, execute the Run_KRAKEN3D_Tagus_Estuary.m program (KRAKEN and FIELD3D are run);
3. Run Plotting_Tagus_Estuary.m

This worflow is similar for the Azores study case (tests/azores/), except that only KRAKEN is necessary to execute.

Data description

• data/bathymetry/EMODNET_DTM_*.nc: bathymetry data from the EMODNET DTM database (after extraction, those two datasets were cropped for the Azores and Tagus estuary regions), that can be accessed at http://www.emodnet-bathymetry.eu;
• data/bathymetry/gebco_azores_2020.nc: bathymetry data from the GEBCO 2020 global grid dataset (https://www.gebco.net/data_and_products/gridded_bathymetry_data/gebco_2020/), used only for the Azores study case;
• data/shorelines/GSHHS_h_L1*: GSHHG shoreline data for obtained from https://www.soest.hawaii.edu/pwessel/gshhg/;
• data/shorelines/CNTR_RG_01M_2020_4326*: shoreline dataset from the GISCO database (https://ec.europa.eu/eurostat/web/gisco/overview), for the Tagus estuary study case;
• data/temperature_salinity/cmems_mod_ibi_phy_anfc_0.027deg-3D_P1D-m_1647891936780.nc: dataset of monthly mean data of 2021 of ocean's temperature and salinity 3D data in the Azores region from the Operational Mercator global ocean analysis and forecast system (https://doi.org/10.48670/moi-00016);
• data/temperature_salinity/global-analysis-forecast-phy-001-024-monthly_1656015476392.nc: 7-day span daily mean temperature and salinity data provided by the operational IBI (Iberian Biscay Irish) Ocean Analysis and Forecasting system data which was extracted for the Tagus Estuary region (https://doi.org/10.48670/moi-00027).

References

[1] The Acoustics Toolbox. Last accessed July 8, 2022: http://oalib.hlsresearch.com/AcousticsToolbox/.
[2] Pawlowicz, R., 2020. "M_Map: A mapping package for MATLAB", version 1.4m, [Computer software], available online at www.eoas.ubc.ca/~rich/map.html.
[3] Roberts, K. J., Pringle, W. J., and Westerink, J. J., 2019. OceanMesh2D 1.0: MATLAB-based software for two-dimensional unstructured mesh generation in coastal ocean modeling, Geoscientific Model Development, 12, 1847-1868. https://doi.org/10.5194/gmd-12-1847-2019.
[4] Stephen23 (2022). ColorBrewer: Attractive and Distinctive Colormaps (https://github.com/DrosteEffect/BrewerMap/releases/tag/3.2.3), GitHub. Retrieved July 8, 2022.
[5] Sergei Koptenko (2022). Sound Speed in Sea Water (https://www.mathworks.com/matlabcentral/fileexchange/4940-sound-speed-in-sea-water), MATLAB Central File Exchange. Retrieved July 8, 2022.