Document Type



Virginia Institute of Marine Science

Publication Date



This dataset includes model input, code, and output used in the publication Birchler et al. (2018, Journal of Coastal Research), which used a coupled hydrodynamic-sediment transport-geochemical model to investigate the roles of resuspension, deposition, on biodiffusion on the behavior of short-lived radioisotopes on the Mississippi sub-aqueous delta, USA. Model development for this project focused on incorporating radioisotope tracers into the sediment transport module in the Regional Ocean Modeling System (ROMS). As described in Birchler et al. (2018, Journal of Coastal Research), the model can account for supply and sorption of radioisotope tracers in the water column; biodiffusion of radioisotope tracers within the seabed; storage of radioisotope activity and inventory in the seabed; radioisotope decay in the seabed; and resuspension and removal of radioisotope tracers.


These files are compressed versions of input files, model code, and output used for an associated publication in Journal of Coastal Research (Birchler et al. 2018). 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: see For information about the Regional Ocean Modeling System (ROMS), its model code and input / output, see

Description & File Name

Input Files

  • Input File – Model Initialization -
  • Input File - Wave Forcing -
  • Input File - Sediment Information -
  • Input File – Model Run Information -
  • Input File – List of variables - varinfo.dat
  • Input File – Options for model compilation - sedbiotoy.h
  • Input File/Model Code: Model grid and wind stresses -
  • Input File/Model Code: Surface tracer fluxes - ana_stflux.h

Model Code

  • Model Code - Script to Compile Model - build.bash
  • Model Code - Model Code Used for Standard Model Run - trunk_sbt2.tar

Model Output

  • Model Output - Standard Model Run -
  • Model Output – High Biodiffusion Rate Version of the Model Run -
  • Model Output – No Biodiffusion Version of the Model Run -
  • Log File of Standard Model Run - ocean_012.out
  • Log File of High Biodiffusion Rate Model Run - ocean_013.out
  • Log File of No Biodiffusion Model - ocean_014.out



Sediment transport model, Mississippi subaqueous delta, radioisotopes; Regional Ocean Modeling System (ROMS)

Associated Publications

Birchler, J.J., Harris, C.K., Kniskern, T.A., and Sherwood, C.R., 2018. Numerical Model of Geochronological Tracers for Deposition and Reworking Applied to the Mississippi Subaqueous Delta. Journal of Coastal Research: Special Issue 85 - Proceedings of the 15th International Coastal Symposium: pp. 456 – 460.


Funding was provided by the U.S. Bureau of Ocean Energy Management (BOEM) (Birchler, Harris, Kniskern), VIMS’ Office of Academic Studies (Birchler), and by sponsors of W&M’s computing facilities, including the National Science Foundation, the Commonwealth of Virginia Equipment Trust Fund and the Office of Naval Research. This work was partially supported by the U.S. Geological Survey, Coastal and Marine Geology Program. Use of firm and product names is for descriptive purposes only and does not imply endorsement by the U.S. Government.