Document Type

Data

Department/Program

Virginia Institute of Marine Science

Publication Date

2019

Abstract

This dataset includes model input, code and output used in the publication Tarpley et al. (2019, Journal of Marine Science and Engineering), which used a coupled hydrodynamic-sediment transport model to investigate the roles of flocculation, bed consolidation and sediment-induced stratification on changes in fine-grained sediment distribution in an idealized estuarine model. The modeling system used in the development was the Coupled Ocean-Atmosphere-Wave-Sediment Transport (COAWST) framework.

Description

These files are input files, model code and output used for an associated publication in the Journal of Marine Science and Engineering (see below). 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 and these files have “nc” as a file extension and can be read using a variety of open source tools: see http://www.unidata.ucar.edu/software/netcdf/docs/ .

The reference run included all three cohesive processes (bed consolidation, flocculation and sediment-induced stratification) and is denoted as "ref". All other runs are indicated by the cohesive processes included in the run, for example oceans_sed_bed.nc is the output file for the model run that incorporates bed consolidation and sediment-induced stratification but not flocculation. The abbreviations are: “bed” for bed consolidation, “sed” for sediment-induced stratification, “floc” for flocculation, “3cls” for 3 sediment classes, and “5cls” for 5 sediment classes. COAWST (Coupled Ocean Atmospheric Wave Sediment Transport) version 3.2 was used for these simulations. For access to the COAWST modeling system source code, see https://coawstmodel-trac.sourcerepo.com/coawstmodel_COAWST/

File | Description

Input Files

  • oceanrst_sed2.nc : Input file – Sediment spin-up output with 11 size sediment classes used for reference case runs
  • oceanrst_sed_floc_3cls.nc : Input file – Sediment spin-up output with 3 sediment size classes used for sensitivity test
  • oceanrst_sed_floc_5cls.nc : Input file – Sediment spin-up output with 5 sediment size classes used for sensitivity tests
  • ocean_ref.in : Input File – Model run information for the reference case run
  • sediment_york.in : Input File – Sediment transport for 11 size sediment class cases
  • sediment_york_3cls.nc : Input File – Sediment transport for 3 size sediment class case
  • sediment_york_5cls.nc : Input File – Sediment transport for 5 size sediment class case

Model Code

  • coawst.bash : Model Code – Script to compile model code
  • estuary_test2.h : Model Code – Header file containing ROMS model implementation setup

Source Code

  • ana_fsobc.h : Source Code – File setting the tidal height on the western boundary
  • ana_grid.h : Source Code – File setting the idealized estuary grid
  • ana_m2obc.h : Source Code – File setting the river discharge
  • ana_tobc.h : Source Code – File setting the temperature and salinity values at the boundaries
  • trunk : Source Code – Directory that contains the ROMS model code

Model Output

  • oceanhis_ref_v2.nc : Model Output – Model output for reference case
  • oceanhis_bed_sed.nc : Model Output – Model output for the no flocculation case
  • oceanhis_bed_floc.nc : Model Output – Model output for the beginning of the no sediment-induced stratification case
  • oceanhis_sed_floc.nc : Model Output – Model output for the no consolidation case
  • oceanhis_floc_3cls.nc : Model Output – Model output for the 3 size sediment class case
  • oceanhis_floc_5cls.nc : Model Output – Model output for the 5 size sediment class case

DOI

Archive DOI: https://doi.org/10.25773/86rw-6393

Keywords

Sediment transport, Coupled Ocean-Atmosphere-Wave-Sediment Transport (COAWST) model, cohesive sediment, numerical modeling, flocculation, bed consolidation, sediment-induced stratification

Associated Publications

Tarpley, D.R.N., Harris, C.K., Friedrichs, C.T., Sherwood, C.R. (2019). Tidal variation in cohesive sediment distribution and sensitivity to flocculation and bed consolidation in an idealized, partially mixed estuary. Journal of Marine Science and Engineering. 7(10), 334. DOI:10.3390/jmse7100334

Publication Statement

Author contributions: 1. Tarpley – Model development, implementation and analysis. 2. Harris – Oversaw all aspects of model development. 3. Friedrichs – Oversaw aspects of experiment design.

Funding

Funding was proved by the National Science Foundation grant number, OCE-1459708.

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