Abstract:
This dataset contains model input, code, and output used in the publication Cui et al. (2021), which describes the development of “OPAMOD." Developed as part of Consortium for Simulation of Oil Microbial Interactions in the Ocean (CSOMIO) to account for the formation of oil-particle aggregates (OPAs), the OPAMOD module incorporates modifications to an existing, population dynamics-based sediment flocculation model. OPAMOD was developed within the Regional Ocean Modeling System (ROMS), as distributed via the Coupled Ocean-Atmosphere-Wave-and-Sediment Transport (COAWST) modeling system. The dataset includes the source code, input files, and model output used to produce the results for the associated publication Cui et al., 2021. Also included are scripts to reproduce the figures presented in the publication. This dataset supports the publication: Cui, L., Harris, C. K., & Tarpley, D. R. N. (2021). Formation of Oil-Particle-Aggregates: Numerical Model Formulation and Calibration. Frontiers in Marine Science, 8:629476. doi:10.3389/fmars.2021.629476.
Suggested Citation:
Cui, Linlin and Courtney K. Harris. 2022. Dataset for: Formation of Oil-Particle-Aggregates: Numerical Model Formulation and Calibration. Distributed by: Gulf of Mexico Research Initiative Information and Data Cooperative (GRIIDC), Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/n7-x78w-kp69
Purpose:
The OPAMOD module has been developed to estimate the formation of OPA by the aggregation of oil droplets and sediment particles. The examples of model runs provided in this dataset were described in the associated publication Cui et al., 2021, where OPAMOD was run as part of a coupled hydrodynamic-sediment transport model. OPAMOD also was used to provide a link between the oil module and the sediment module within the full CSOMIO coupled ocean-oil-sediment- biology model system that was described by Dukhovskoy et al., 2021.
Data Parameters and Units:
In addition to the usual COAWST variables, the sediment variables are mud_##, suspended cohesive sediment size classes 1-30 [0.03 mm - 0.14 mm, kg/m^3], mudfrac_##, cohesive sediment fraction size classes 1-30, and mudmass_##, cohesive sediment size classes 1-30 [kg/m^2], sediment bed layer thickness [m], sediment layer age [s], sediment layer porosity, sediment median grain diameter [m], sediment median grain density [kg/m^3], sediment median grain settling velocity [m/s], sediment median critical erosion stress, bottom ripple length [m], bottom ripple height [m], bed wave excursion amplitude [m], apparent bottom roughness length [m], Nikaradse bottom roughness length [m], biological bottom roughness length [m], and active layer thickness [m].
Compressed files with the .gz file extension can be opened with Gzip GNU software (open source). Compressed files with the .tar file extension can be opened with Gzip Tar software (open source). Many of the input and output files use the NetCDF (Network Common Data Form) file format. These have "nc" as a file extension and can be read using a variety of open-source tools: please see http://www.unidata.ucar.edu/software/netcdf/docs/. For information about ROMS, its model code and input/output, see http://www.myroms.org/. For more information about COAWST, see https://www.usgs.gov/software/coupled-ocean-atmosphere-wave-sediment-transport-coawst-modeling-system.
Methods:
Source code developed within the ROMS ocean model distributed within the COAWST modeling framework. Model input generated using Matlab and ASCII text editors. Model output generated by running the ROMS model. Details are in the associated publication, Cui et al. (2021).
Provenance and Historical References:
Dukhovskoy, D. S., Morey, S. L., Chassignet, E. P., Chen, X., Coles, V. J., Cui, L., Harris, C.K., Hetland, R., Hsu, T.J., Manning, A.J., Stukel, M., Thyng K. and Wang, J. (2021). Development of the CSOMIO Coupled Ocean-Oil-Sediment- Biology Model. Frontiers in Marine Science, 8:629299. doi:10.3389/fmars.2021.629299.
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